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AIDA Array Compare User's Manual

1. Footnote M author Iw last change time M software version Figure 2 88 Protocol Print Section Page Layout In the Edges part you can specify the margins in cm or inch for the printout In the Header part you can select whether to include the file path the page number and or the current date in the header of the printouts In the Footnote part author last change time and software version can be selected to appear in a footnote Using Array Compare 69 Print Options for Images Window Selecting the Images option you can specify the paper orientation for the printout as well as the items you want to print Protocol Print AD Aj Frint Preview Soo Mages WLS Format Portrait C Landscape Automatic Size C ho A o E Frint MW Parameter W Images W Overlays W Grayscale v Scales Figure 2 89 Protocol Print Section Images The printout result depends on the current Image Display settings used in the Display Control toolbox i e for example if you have chosen Overlaid Display in the Display Control toolbox the images are printed overlaid accordingly If you have set Image Display to Tile Vertical or Tile Horizontal the images are printed one after the other In the Format part select the paper orientation for the printout Portrait or Landscape The size of the image can be automatically adjusted to fit the page Automatic Size Alternatively you can enter the zoom f
2. Analysis Table Clauses X Ratio Narmalized Bkd 03 E cea OK Cancel Figure 3 17 Defining Filter Rules The resulting Array Analysis Table can be exported to a file for post processing Comparing Arrays 107 108 AIDA Array Compare User s Manual Appendix 4 Formal Description of Normalization Let Ref r i 1 N denote the set of all reference clones within a filter The normalization constant for a filter is determined by averaging the background corrected intensity values of the clones from these set N C dtr BG i l I r Intensity value for clone r B r Background value for clone r The normalized values for the clones are the relative signal values with respect to this constant I clone ne N clone 2 These values are shown in the Normalized Bkg 9 o column of the Array Results Table in AIDA Array Metrix 109 In AIDA Array Compare the comparison of two filters are now processed on the background corrected normalized values of the two filters if you have selected the Normalized Bkg values for comparison N2 clone Nl clone R clone R clone Ratio value for a clone N1 clone Normalized background corrected value of clone in filter 1 N2 clone Normalized background corrected value of clone in filter 2 Using the definition stated above the formula can be rewritten by I2 B2 N2 C2 _ I2 B2 Cl Nl 11 Bl II B1
3. Tile Horizontal and Tile Vertical places them side by side and on top of each other respectively Both options use grayscale for displaying the images The Overlaid Display option shows the two images superimposed on each other in false color display EZ Images onco a cr ary Figure 2 26 Overlaid Display Example Using Array Compare 27 Quantile Plot Window In the Quantile Plot window the values of the array comparison master and the values of the client are each sorted by quantity and then plotted against each other Using this data view you can easily check for saturation issues occurring in slide evaluations Generally the Quantile view allows conclusions on the normalization quality To display the Quantile Plot window select Quantile Plot from the View menu view Window Help Images Array Result Table Array Correlation Schematic Displav Schematic Histagram Analysis Table Probe Table Probe Correlation Figure 2 27 Selecting Quantile Plot 0 01 0 1 1 1 100 1000 10000 Master Normalized Bkg Figure 2 26 Quantile Plot Windows Example 28 AIDA Array Compare User s Manual Array Result Table Window This window shows the results of the array comparison in tabular form To display the Array Result Table window select the Array Results option from the View menu view Window Help Images Guantil Plot kr Correlation Schematic Displav Schematic Histogram Analvsis Table
4. 02 12 12 i ae a RNV E dd Figure 2 33 Interlinkage between Images and Array Result Table Window You can select the number and type of columns you want to display using the shortcut menu of any column in the window see below If you want to change the column order click the heading of the column to be moved hold down the mouse button and drag to the desired position in the table Release the mouse button Bi array Result Table onco a c ary Ioj x Ma er Drea ien 0 xl 1s e Index Lael a afoma Jaa 1 oenis Master Ir moa sa 2 mema ts Es soos fa alama ss ejm s mens ss mos f s mans fa 2 92 oma Figure 2 34 Changing the Column Order Indes Label Type rs Using Array Compare 33 To change the column width position the mouse pointer at the border of the column whose width you want to change then click and drag the border in the appropriate direction Release the mouse button ch Array Result Table onco_a_c ar m x Index Type Label Maste Client Integral Area Ratio m PSL mrr 3 Mz ali EN i Array Result m onco a c ary B x Index Type Label SERI Integral Area Hatia FSL f L mrr T L i EE pm Table onco a c ary mi x Master Integral amp rea PSL mrr L ee iac m m Client Integr PSL rni Figure 2 35 Changing Column Width
5. AIDA Array Compare User s Manual Client Mormalized Bk gq 95 1000 100 0 1 0 01 0 001 0 01 0 1 10 100 1000 Master Normalized Bkg Part Number 2003 09 2 1 2003 raytest IsotopenmeBgerate GmbH Benzstr 4 D 75334 Straubenhardt Germany All rights reserved This product or document is protected by copyright and distributed under licenses restricting its use copying distribution and decompilation No part of this product or document may be reproduced in any form by any means without prior written authorization of ray test and its licensors if any RESTRICTED RIGHTS LEGEND Use duplication or disclosure by the government is subject to restrictions as set forth in subparagraph c 1 11 ofthe Rights in Technical Data and Computer Software clause at DFARS 252 227 7013 and FAR 52 227 19 The product described in this manual may be protected by one or more U S patents foreign patents or pending applications TRADEMARKS AIDA AIDA Array Metrix and AIDA Array Compare are trademarks or registered trademarks of raytest in the United States and may be protected as trademark in other countries All other product service or company names mentioned herein are claimed as trademarks and trade names by their respective companies THIS PUBLICATION IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTAB
6. Column 2 Subgrid column position of the dot 2 level potential reference column for name table import Column 3 Subgrid column position of the dot spot matrix level potential reference column for name table import Label 1 Label first level Label 2 Label second level Label 3 Label third level Row Label 1 Subgrid label of the dot row component 1 level Row Label 2 Subgrid label of the dot row component 2 level Row Label 3 Subgrid label of the dot row component spot matrix level Subgrid label of the dot column component 1 level Suberid label of the dot column component 2 level Subgrid label of the dot column component spot matrix level Name of a dotted sample imported from name table column name can be adjusted and cells can be linked to external database by the user via column shortcut menu command ID number of a dotted sample imported from name table column name can be adjusted and cells can be linked to external database by the user via column shortcut menu command User definable columns for name table import purpose column name can be adjusted and cells can be linked to external database by the user via column shortcut menu command where data denotes one of the following selectable from the Data drop down menu of the Array Comparison toolbox Table 2 2 Data Type Integral Integral Bkg Integral Area Data Types Short Explanation Integrated raw intensity of a spot Integral bac
7. Shortcut Menu of the Array Result Table Window Each column in the Array Result Table has a shortcut menu attached T Array Result Table onco_a_c ary m x Master Integral amp rea Client Integral Area Ratio Integral Area Sort ascending by Master Integral Area Sort descending by Master Integrall rea MAN 3 8s nsn 8 5b oam T 3a oam L 015 IM H Figure 2 36 Shortcut Menu Array Result Table Select Master Integrall rea Hide Master Integral 4area Settings of Master Integral Area One lined Header Select Ses 34 AIDA Array Compare User 5 Manual The table can be sorted by any value column in ascending order A to Z or zero to 9 or descending order Z to A or 9 to zero Just choose the appropriate menu item Sort ascending by Sort descending by wv Sort ascending by Integral Bkg h Sort descending by Integral Bkg Select Integral Bkg Hide Integral Bkg Settings of Integral Bkg One lined Header Select Columns Figure 2 37 Sorting Table This is especially of interest for finding highest intensity values and for identifying the highest absolute or relative deviations in double dotted samples for quality control The Select Unselect options of the shortcut menu are used to select unselect a column to export The column heading of selected columns are highlighted To hide a column select the Hide option from its shortcut menu You can recover h
8. The background thresholds Master Cut Off and Client Cut Off divide the correlation plot into four parts Comparing Arrays 99 1 Master value lt Master Cut Off and client value lt Client Cut Off Both master and client value are within the background range 1 e their ratio cannot be determined In this case Array Compare sets the ratio value to 1 expression value No 2 Master value lt Master Cut Off and client value gt Client Cut Off In this case only the master value is within the background range whereas the client value is above the background threshold Their ratio cannot be determined but since client s measurement value can be determined in contrast to case 1 above the ratio value is set to the predefined constant Max Ratio expression value On 3 Master value gt Master Cut Off and client value Client Cut Off This is the opposite case of 2 with the value of the master array above the background threshold and the client array value indeterminable The ratio value is set to Max Ratio expression value Off 4 Master value gt Master Cut Off and client value gt Client Cut Off Both values are above the background thresholds so their ratio is determinable client value master value If ratio value gt 1 the expression value is set to ratio value and if ratio value lt 1 the expression value is set to ratio value Note For values which are within the range of the expres
9. section above Ratio Comparison Cut Of Parameter Threshold 3 0 5tdD ev g Fatio Comparison Cut Off Farameter has Ratio 100 Ratio Cut Off C explicit Threshold by Bkg Deviation Schematic Display onco a c ary 01 2 03 04 O5 a p e H ot ee ERE a Ea E E e ARE a NE E cee eee Array Comparison Master Array Onco_a adf over onco_a int Data Normalized Bkg m ratio hd Onca c adf over onca c inf Add Remove ial x 0G OF O06 ag 10 11 1 2 gc Wu SEE HHE H d ea Molte TM a eee etti ces kee t ntt E E Ea LEN EM LIII TBBRBGA n n n schematic Display Ratio of Mormalized Bkg Data E Colors JE 2 0000 E 2 0000 B Figure 3 12 Schematic Display of Loaded Arrays With Toolbox Default Settings 102 Usually you do not have to change the default settings of the Ratio Comparison panel on the Array Comparison toolbox They are suitable for most cases But in some special cases you might want to adjust the settings following Step 2 AIDA Array Compare User 5 Manual 2 On the Ratio Comparison panel select the Parameter tab click the explicit Threshold radio button and enter a value for Max Ratio 3 Select the Cut Off tab and set Master Cut Off and Client Cut Off to 5 10 Ratio Comparison Schematic Display onco a c ary Cut Off Parameter Mas Ratio Ratio Cut Off Ratio Comparison Cut Off Parameter pe
10. C2 In Array Compare you can introduce expression values 2 and 0 5 for instance for this ratio values to filter out and mark the up and down regulated genes 110 AIDA Array Compare User s Manual
11. Exclude from Schematic iv Empty Dots Iv Guide Dots Background Dote Exclude From Schematic Section Reference Dots v Bad Quality Dots Actual Probe Actual Probe Section Schematic Display Ratio of Integral Data X Y Colors 76 800005 zi 40000 E Schematic Display Section 2 0000 E 4 0000 8 0000 Figure 2 75 Array Schematic Toolbox Overview Using Array Compare 61 raytest Settings made via the Array Schematic toolbox affect not only the Schematic Display window but also the Schematic Histogram as well as the Array Correlation plot Furthermore the ratio and expression values recorded in the Array Result Table are affected by the Array Schematic toolbox settings too Exclude From Schematic Section In the Exclude from Schematic section of the Array Schematic toolbar you can select some dot types for exclusion from the schematic analysis These types are empty dots guide dots and bad quality dots Exclude from Schematic Iv Empty Dots v Guide Dots Background Bots Reference Dots Iv Bad Quality Dots Figure 2 76 Exclude From Schematic Section Values excluded via the Exclude from schematic option appear in gray in the Schematic Display window and are marked with a cross to avoid confusion with real gray scale values 9 Schematic Display onco a c ary Bl x 01 02 03 um n Figure 2 77 Dots Excluded From Schematic 62 AIDA Arra
12. Mando MSHU a5 a oie te See eta Gira wa Qe ed d sn enn bed acus Bre ca ou e ee 19 Toolbox Control Menu 0 ia oui ER eg Ee RE ERRARE EA ATE 20 OOM ar SURO UNS 4 ae S oo ooo atio is Dosen aoo tod a ela aceon Sarees 20 Pile Options lett Sec ofi aed ae bec boe che thee ee OEC ea 21 Visual Tools middle section scott tco re tot tn dea TERCERO n Bw de 21 Evaluation Option right section first half 0 0 0 0 0 cee eae 24 Toolbox functions right section second half 0 0 0 000 000 ee 24 Shortcut NGBUS oes auod ed ardor Sle wo deutrint A Shulkin Ge peer desde 24 iii Data Windows in Array Compare 0 000 cc cee eee ees 25 Imases WIDnde We uec 35 ors a a Sg as uen we odo Sr aa ore ae ato Se 26 Shortcut Menu of the Images Window 00 cee eens 27 Quante Plot WindOWs ass race pa ard add a oae Dots aae t ee eed 28 Array Result Table Window 0 0 cc eee es 29 Data D SCEIDIIOTE eaae Ru Gos ae eae eee arate ras sae ara at ende ela ee eg 30 Shortcut Menu of the Array Result Table Window 34 Array Correlation Window 0 cc cee eee E E A 37 Shortcut Menu of the Array Correlation Window 0005 41 schematic Display WIDdOW x sod rr Eve ore i eR WEES eee 43 Schematic Histogram Window 0 eens 45 Shortcut Menu of the Schematic Histogram Window 47 Analysis Table Window uae RR bep obo oe Poe b uU VOS 48 Prope Table MAB
13. Protocol Print JF Probe Table Format Portrait C Landscape f Full Table Rows above Figure 2 95 Probe Table Print Options 76 AIDA Array Compare User 5 Manual Print Options for Probe Correlation The Probe Correlation button on the Protocol Print toolbar allows you to configure the layout setting for the Probe Correlation window You can select the paper orientation Portrait or Landscape by clicking the appropriate radio button in the Format section The Graphic option in the Print section enables or suppresses the print output of the graphic displayed in the Probe Correlation window Protocal Print amp amp Print Preview 3 Probe Correlation Portrait C Landscape g Print Iv Graphic Figure 2 96 Probe Correlation Print Options Print In AIDA Array Compare there are two ways for printing your image and evaluation data 1 Select the Print option from the File menu or 2 use the Protocol Print section on the Publishing Layout toolbox The Print command of the File menu allows you to print your data on the fly without permanently storing the layout printing settings whereas the Protocol Print panel provides you with a complete set of printing features which includes saving the setting with the data file for reasons of reproducibility Using Array Compare TI Selecting the Print option from the File menu opens the Print Array Compare dialog box allowing you to c
14. Windows Metafile format Exporting Schematic Histogram To export the Schematic Histogram On the File menu click the Export menu item and then select Schematic Histogram from the cascading menu In the Schematic Histogram Export dialog box that appears enter a name for the export file Schematic Histogram Export onco_a_c ar xl Save in E Examples t E amp 3 E an onco correlation wmf File name onco schematic histogram Save as type windows Metafile E Cancel Figure 2 106 Schematic Histogram Export dialog box Complete the export action by clicking the Save button The data are saved to a file in the Windows Metafile format Exporting Analysis Table To export the Analysis Table On the File menu click the Export menu item and then select Analysis Table from the cascading menu In the Analysis Table Export dialog box that appears enter a name for the export file 84 AIDA Array Compare User 5 Manual Analysis Table Export onco_a_c ar File name Jonco analysis table Save as type Table ASCII File Cancel Figure 2 107 Analysis Table Export Dialog Box After you confirmed the export by clicking the Save button the Analysis Table Export Options dialog box appears allowing you to set further option for the export of the analysis table Analysis Table Export Options X Range M Header Cancel 6 All Rows Selected Rows Cancel AllColumns Select
15. ASCII text file Exporting Probe Correlation To export the Probe Correlation display On the File menu click the Export menu item and then select Probe Correlation from the cascading menu In the Probe Correlation Export dialog box that appears enter a name for the export file Complete the export action by clicking the Save button The data are saved to a file in the Windows Metafile format 86 AIDA Array Compare User 5 Manual Importing Array Evaluations To add an array client to the master for comparison click the File menu and then select Array Evaluation in the Import cascading menu Choose the array file you want to import from the file list in the Array Evaluation Import dialog box that appears and click Open Array Evaluation Import onco_a_c ar xl Look in Cy Examples amp ter E3 a Ag test adf 28 Paols2 adf se Clontech Large Array adf se Rat adf Onca a adf se Simple Array adf 39 Poals1 adf 1 Poolsic adf File name Onco_a adi Files of type alba Data Format Cancel Figure 2 110 Array Evaluation Import Dialog Box Alternatively you can click the Add button on the Array Comparison toolbox to open the Array Evaluation Import dialog box and select your client array file Importing Name Tables The Name Table Import option is intended for easy import of names and ID numbers of samples like clones sequences oligos etc Usually importing name tables is p
16. ASCII File format Name Table Import onco a c ary aj xj Look in 3 Examples gr E3 Clontech Large Array txt Clontech Hbroad Large Array Ext Clontech Hcancer Large Array Ext demo txt onco txt File name Clontech Hcancer Large Array tet Files of type Ara Mame Table hs Cancel Figure 2 111 Name Table Import Dialog Box 88 AIDA Array Compare User 5 Manual The Import Name Table dialog box appears allowing you to specify the options for the name table import via spin boxes and tabs In the lower part of the dialog box the import source table is displayed Import Name Table onco_a_c ary I Delimiter Link 1 Link 2 Link 3 Link 4 Import by Global Label Column 2 B Mame 1 Gene Mame cell divisio cyclin depen cell divisio cell divisio 8 cell divisio cell divisio g protein seri 8 cyclin depen Table Header Mame Link GenBank Acce SwissProt Ac Atlas Human 05360 POB4S3 Ala MEB520 P2494 Alb 6635 QO0826 Alc M14505 F11802 0005 Ald AXbb354 QO0835 Ale 66365 QO0834 Alf L20320 P0613 Alg L34051 13318 Alh Figure 2 112 Import Name Table Dialog Box 3 Select the type of delimiter TAB comma semicolon or SPACE from the Delimiter drop down list 4 Specify the import method using the pull down menu below the Delimiter drop down list Import Name Table onco a c ary Delimiter lt TAB Link wI t by Global Lab
17. Array Histogram and Array Analysis Table information can be selected in the left part of the Print Array Compare dialog box In the right part of the dialog box Parameter and Image Options section you can select Whole Image or Window Content from the first drop down menu Choose Landscape or Portrait format from the second drop down menu Further the printing of Overlays Grayscales Scales and Overexposed can be enabled by checking the respective options The printout can be configured to automatically fit to the page or the relative size of the image representation can be selected in In the Analysis Table Options and Probe Table Options sections you can specify to print the entire tables full table or just a part of them rows above as well as the paper orientation landscape or portrait The paper orientation can also be specified for the Schematic Display output using the drop down menu in the Schematic Display Options section Preview As for printing in AIDA there are two ways of previewing pages before they are actually printed 1 Using the Print Preview option of the File menu or 2 using the Preview button on the Publishing Layout toolbox The Print Preview option of the File menu opens the Preview dialog box which allows you to specify the layout settings for the preview The options presented here are the same as in the Print Array Compare dialog box and those selectable from the various sections of the Publishing La
18. Row Index spin boxes for Import by Global Position or the Column and Row spin boxes for 1 Level 2 Level Spot Level if Import Import Name Table onco a c ary lt TAB bu E mm Using the tabbed panel of the Import Name Table dialog box Link 1 Link 2 Link 3 and Link 4 you can specify up to four source columns to be imported into your target table Furthermore the tabs allow you to enter a user defined name for the column header of the resulting target column In addition the cells of imported columns Name or ID for example can be hyperlinked to internal or external databases so you can search the linked databases for the name or ID by just clicking the respective cell in the Array Result Table Name and hyperlink of imported columns can adjusted via the Settings of command selectable from the shortcut menu of the respective column Link 1 Link 2 Link 3 Link 4 coum P E l Table Header Name Link http Awww CHAM Ah gowentres querntegi ctmd se Figure 2 116 Link Panel 6 Enter the number of the source table column you want to import into your target table using the Column spin box of the Link 7 tab Look up the column number in the source table display shown in the lower part of the dialog box Note Entering the column number 0 in the Column spin box of a Link n tab indicates that no source column has been selected for import on this particular tab 7 Enter a name for the co
19. of the Log ratios of the two arrays gray line and the data mean thresholds color coded lines configurable via the Array Schematic toolbox are represented see the Reviewing Array Comparison Data section for a more detailed description Using Array Compare 51 To open the Probe Correlation window Select the Probe Correlation option from the View menu view Window Help Images Quantil Plot Array Result Table Array Correlation Schematic Display Schematic Histogram Analysis Table Probe Table Figure 2 62 Selecting Probe Correlation View Probe Correlation Compare U nco a amp c ary Client Mormalized Bk gq 95 1 1 100 1000 10000 Master Normalized Bkg Figure 2 63 Probe Correlation Window Example The Probe Correlation window provides the same set of display controls as the Array Correlation window so please refer to the respective description in the Array Correlation Window section for further details 52 AIDA Array Compare User s Manual Toolboxes of Array Compare In Array Compare there are five toolboxes available Array Comparison Display Control Array Schematic Array Analysis Table e Publishing Layout You can access these five toolboxes via the Evaluation menu or by clicking the appropriate button on the toolbar Evaluation Options View la Array Comparison Display Control Array Schematic w Array Analysis Table Publishing Layout Figure 2 64 Eva
20. on oie Gk Ae ce Coates cone rc Setting up and Reviewing Array Comparisons 0 0 Ratio Comparison Example Procedure 0 0 0 0 00 eens Appendix Formal Description of Normalization 0 0 0 0 0 0 00 eee eee eens Contents vi AIDA Array Compare User s Manual Introduction Overview AIDA Array Compare is intended for comparing two arrays that were both obtained by AIDA Image Analyzer s Array Metrix module AIDA Array Compare provides a set of visual tools allowing you to display the two arrays in question as well as the result of the comparison in graphical and or tabular form You can compare arrays using schematic views correlation plots or data tables which can be configured by the user according to their needs All data views are interlinked meaning for instance that two arrays can be moved zoomed and positioned simultaneously System Requirements AIDA Array Compare s minimum system requirements are as follows e Intel Pentium compatible CPU One of the following operating systems Microsoft Windows 9x Me Microsoft Windows NT 4 0 Microsoft Windows 2000 Table 0 1 Memory Requirements Windows NT 4 0 Windows 2000 Windows XP minimum 128MB 128 MB 256MB recommended gt 256MB gt 256MB gt 512MB CD ROM drive Graphics adapter capable of displaying at least 1024 by 768 pixels in High or True Color mode 17 color monitor 21 color monitor recommended Ins
21. the automatic filtering process for analysis result values provided by AIDA Array Compare Filter E dit Integral PSL 60 0 or IntegraliArea PSLimin 60 0 Figure 2 84 Filter Section With Rules Assigned The automatic result value filtering process 1s based on rules defined by the user There are no built in default filtering rules so unless you define a specific rule for filtering no automatic filtering 1s applied The filter to be specified consist of a list of conditions Alternatives concatenated by an OR operator An Alternative is a AND linked list of conditionals for evaluating the data values of a particular spot The filter rules you define are Permission rules Values that do not meet the conditions stated in the rules are blocked from being displayed in the Analysis Table window 66 AIDA Array Compare User 5 Manual To enter a rule statement 1 Click the Edit button on the Filter panel The Array Analysis Table Clauses dialog box appears 2 On the Alternatives panel click Add This adds the phrase 1 Clause is to the Alternatives list panel 3 Then click the Add button on the Clauses panel Array Analysis Table Clauses x Alternatives Clauses 1 Clause list Add Delete k Modity Delete Figure 2 85 Adding rule clauses This opens the Analysis Table Clauses dialog box which allows you to define your rule expression Analysis Table Clauses 1 x 4 Analysis Table Clau
22. useful if you want to export the comparison data to another program post processing these data e g for cluster analysis Since these programs usually accept numerical data only and since calculation of ratios of values within background range does not yield reasonable results Array Compare sets the ratio value to Max Ratio if the ratio calculation results in infinity In the majority of cases it is reasonable to set the Max Ratio value to 100 58 AIDA Array Compare User 5 Manual Display Control Toolbox This toolbox is used to control the appearance of the images on the screen To display the Display Control toolbox On the main menu click Evaluation and then click Display Control Alternatively you can select the Display Control button on the toolbar Ei Display Control BE E inverted loo Image Display Control Panel Master Z Client Transfer Master Client Transfer Control Panel Quantum level M Range fir gj se B automatic full Gamma xj gt Figure 2 72 Display Control Toolbox Overview Image Display Control Panel With the Image Display control panel of the toolbox you can specify the arrangement of the two Images window panes by clicking the appropriate button Image Display i inverted Overlaid Display Button Tile Vertical Button Tile Horizontal Button Figure 2 73 Image Display Control Panel Overview The Tile Horizontal Tile Vertical a
23. 12b 1 0000 Master Normalized Bkg Figure 2 23 Data Windows Using Array Compare 25 To access these data windows select the appropriate entry Images Quantil Plot Array Results Array Correlation Schematic Display Schematic Histogram Analysis Table Probe Table and Probe Correlation respectively from the View menu view Window Help Images Quantil Plot Array Result Table Array Correlation Schematic Display Schematic Histogram Analysis Table Probe Table Probe Correlation Figure 2 24 Selecting Entry From View Menu Images Window The Images window provides you with a representation of the Array Comparison data on the raw data level It shows the image raw data together with the array overlays from which the data are calculated Although it might not always be on top it is always open In AIDA Array Compare the Images window is bipartite one pane for the array comparison master and one for the client Images onco_a_c ary Mel x EX DOES RE iii a a ame me or tri ee pe oe igen a m 5 m 4 7 n Ms Tt Figure 2 25 Images Window Example 26 AIDA Array Compare User s Manual 2 raytest To copy the content of the Images window to the clipboard select the Copy Content option from the Edit menu Shortcut Menu of the Images Window The shortcut menu attached to the Images window provides three options for arranging the two panes of the window EZ Images onca
24. 3 Level Spotting Fant Arial Size eo r 1 1 print Bj Figure 2 6 Image Overlays Dialog Box The current settings can be saved in the Preferences under a user defined name to be available for further evaluations of similar images Preferences ed Figure 2 9 Preferences Dialog Box 16 AIDA Array Compare User s Manual Select the path for the program configuration files using the Configuration Path option x Configuration Path e iProgram Filesi config La a E c WINE d VNLT EJ a Anwendungen 9 Frogram Files C3raytest Aida Array Compare dev 3 20 enmt cr Projekte Cancel Figure 2 10 Program Configuration Path Dialog Box In this directory all preferences files and other definable settings are stored Use the Image Search Path option to specify the default locations of image files you can keep the images on CD while the evaluation file is stored on the hard drive since AIDA Array Compare does not copy the raw image data into the Array Compare file Multiple search paths can be defined Image 5earch Path X Search images in Directories c WIN Ge Sq Wil ooo Ea Anwendungen E amp Pragram Files CX ravtest Aida Array Compare de ux Program include subdirectories ESf Projekte Figure 2 11 Image Search Path Dialog Box Using Array Compare 17 The Autosaving option allows you to save your current work in the background so that there is always a recent b
25. 9 Column Settings Dialog Box Name Column Instead of decimal digit specifications you can edit the column s default name and enter a URL Uniform Resource Locator to link the column s cells to internal or external databases see the Importing Name Tables section for details Use the One lined Header Two lined Header option to reduce or expand the column heading by one line the second line indicates the units of measurement To select the columns that should be displayed in the table choose the Select Columns option Sort ascending by Master IntegrallArea Sort descending by Master Integral area Select Master Integral area Hide Master IntegrallArea Settings of Master Integral Area One lined Header a Figure 2 40 Select Columns Command of the Shortcut Menu 36 AIDA Array Compare User 5 Manual A dialog box appears displaying two lists titled Show Columns Hide Columns Select the columns you want to show or hide and click the appropriate arrow symbol to transfer the items between the two lists To unselect a particular item just click it again Columns Selection X Show Columns Hide Columns Label 3 Row Index Column Index Master Integral Area PSLimin not used Client Integral Area PSL mrmrn not used Ratio Integral Area Expression Master Quality Client Quality Mame ID cancel Figure 2 41 Columns Selection Dialog Box Array Correlation Window In the Array Correlation window the d
26. Comparison toolbox Ee Images noname TE FEE Ge ee EHAE MA HE Ge a EE SE BE B D E BA E BB EEEE Sh ie Se tf id Ea Ta ee a a E Master Array Onca a adfaoveronco a inf Figure 3 2 Master File Loaded 3 Perform one of the following steps to load the comparison client array Select Array Evaluation from the Import cascading menu of the File menu Click the Add button on the Array Comparison toolbox E Array Comparison Master Array Onco_a adf over onco_a int Data Normalized Bkg isl ratio id Remove Figure 3 3 Adding Client Array 94 AIDA Array Compare User 5 Manual p Z y raytest a This opens the Array Evaluation Import dialog box Array Evaluation Import noname ajx Look in a Examples t E EJ E Ag Eest adf E Pools2 adf Clontech Large Array adf Rat adf Simple Array adf File name Onco_c ad Files of type ADA Data Format Cancel Figure 3 4 Selecting Client Array File 4 Select the appropriate client array file from the file list and click Open The comparison client is loaded into the second pane of the Images window iol x ki E ETET T JH TUE TI x Figure 3 5 Client Loading Completed Comparing Arrays 95 Normalization For the comparability of the results of the two arrays a normalization of an individual result set is necessary AIDA Array Compare offers three methods of normalization which can be select
27. ES M Logarithmic v Automatic Figure 2 50 Data Scaling Dialog Box Using Array Compare 4 Here the Minimum and Maximum value of the x axis Master Normalized Bkg and y axis Client Normalized Bkg can be selected In addition you can enable logarithmic representation and automatic scaling of either axis separately by checking the respective option Logarithmic and Automatic below the Minimum and Maximum spin boxes Choosing the Grid option opens the Grid dialog box which allows you to lay grids over both axis that are an extension of either the big or the small ticks on the axes SS 5 Vertical Mone C Big Tics C Small Tics Harizantal Mone C Big Tics C Small Tics Cancel Help Figure 2 51 Grid Dialog Box 42 AIDA Array Compare User s Manual raytest Schematic Display Window To open the Schematic Display window choose Schematic Display from the View menu Images Quantil Plot Array Result Table Array Correlation c Displa matii he s chematic Histogram Analysis Table Probe Table Probe Correlation isplay Command from the View Menu Figure 2 52 Choosing the Schematic D All f the array ing o l color draw des you with a schematic i fic data range are represented by spots of ident dow prov The Schematic Display win data with 1Ca in a speci ini i 9 E a_i Schematic D
28. File before a new evaluation can be started raytest Data Structure All information processed by AIDA Array Compare is based on array data obtained by AIDA Array Metrix Therefore the only available file format for loading array data is the AIDA Data Format adf This file format is generated by AIDA Array Metrix and contains all information related to the array and its underlying original image data overlays image representation result data etc AIDA Array Compare stores its comparison data in a separate file using its own AIDA Array Compare ary format The original array data are left unchanged The array comparison data file contains no raw image data but symbolic links to the respective image files Therefore if you want to move the comparison data file together with the corresponding image files to another location you have to move the image files manually using the Windows Explorer Irrespective of the directory paths saved in the comparison data file Array Compare uses the current path of the Array Comparison Data file in the first place If Array Compare cannot find any image files the path saved with the comparison data will be searched instead If this is not successful the search path specified via the Image Search Path entry of the Option menu is tried If there are still no image files found the user is prompted for the path On loading array files into Array Compare the program copies all the relevant arr
29. IDA Array Compare selecting is done simultaneously in both images with respect to the array location on each image The same is true for all other data windows aiel EI fame empty o Figure 2 20 Using the Selection Tool 22 AIDA Array Compare User s Manual When the Zoom tool is activated every click into one of the image windows enlarges that part and the corresponding part of the window simultaneously centered around the mouse position by a factor of two leaving the window at the same size Right click to zoom out in the same steps Figure 2 21 Using the Zoom Tool The Zoom tool can also be used in data windows Click in the upper left corner of the area you want to enlarge hold down the mouse button and drag to the lower right corner Upon release the selected area will be displayed enlarged in the same window The right mouse button is used to zoom out again The Move tool can be used to view parts of the window content that lie outside the window e g for a zoomed image When activated you can click at any position in the image hold down the mouse button and move around the window content with the pointer The Move tool does not work in data windows Usually the Eyedropper tool allows you to examine pixel values at mouse position In some graphical windows selecting the pipette shaped symbol enable cross hairs attached to the pointer which runs across the curve displayed in the data window while m
30. ILITY FITNESS FOR A PARTICULAR PURPOSE OR NON INFRINGEMENT THIS PUBLICATION COULD INCLUDE TECHNICAL INACCURACIES OR TYPOGRAPHICAL ERRORS CHANGES ARE PERIODICALLY ADDED TO THE INFORMATION HEREIN THESE CHANGES WILL BE INCORPORATED IN NEW EDITIONS OF THE PUBLICATION raytest MAY MAKE IMPROVEMENTS AND OR CHANGES IN THE PRODUCT S AND OR THE PROGRAMS S DESCRIBED IN THIS PUBLICATION AT ANY TIME Contents 1 Introduction 5 D aU W CP 5 System ROquire ments esses osse hdd AO EE aon bomen tes Aa hae bi Re 5 Installing AIDA Array Compare 0 nee eens 6 Wonele ProtecuOn s Su s cade a ee um Khe bee d edd eee tee wee Ee 6 LACENSING Key us cine ata dre ir ea d hae ee aes ere ee nr A e Regen 7 PRO NOTING Cus eaa eeu Rede at cn ot dui Pater ee ate nies Cau ae eee MruL Eo 8 2 Using Array Compare 9 Programi SUUCIIIC ss dun DRESS PEU ESSE bee ete d wes 9 IPSIS TRUE ERE TNR ERO TEES TI TT IU eet ee tote ae 10 OVeLllaySoc caue d Eder ES VuSudeuEcbeSLLpbeREIVIA ORDRE Adds Sed 12 Matt Mensa s ee ene de eder edet be encodes odeur dez are wdestire w deer E 12 FEM 6 ntact di ei deed 0 yin aie A Gag al Bald Uns el at GB hte hake 13 ECCE DOR soe evs bere cite lows anie und adl asain Us ta er es arcu doe aw 14 Evaluaton Memibaus uua ee ver Scie bee Oe iw d do Save Se dei oleae Shes 15 Options Ment terii ireti Sod be de Mian b dete Lebe sm Sodan dcin de tdi Acad 15 Me MOD sm bares 2 5555 AG anne rtt eeu da ahi rbi nd Ad pars uoi me tuts tm eta 18
31. Minimum and Maximum value of the x axis Log Ratio of Normalized Bkg and y axis Counts can be selected In addition you can enable automatic scaling of either axis separately and logarithmic representation for the y axis only by checking the respective option Logarithmic and Automatic below the Minimum and Maximum spin boxes Analysis Table Window In contrast to the Array Result Table window which lists the analysis results for the entire array the Analysis Table window is used to display analysis results for a subset of the array O x Type Master Marmalized Bkg Client Normalized Bkg Hat I Analysis Table onco_a_c ary foma smagia 0 0 0 07 a 00000 y EE ae o BjADe Empty Sjmamieb 000 d 7 moamaTa doa E pcm c Gel P Figure 2 59 Analysis Table Window Example You can define those subsets in two different ways manually or by filtering using user defined rules for details see the Array Analysis Table Toolbox section of this manual The Analysis Table window provides the same set of display controls as the Array Result Table window so please refer to the respective description in the Array Result Table Window section for further details 48 AIDA Array Compare User 5 Manual Probe Table Window The Probe Table window lists the ratios of the averaged master and the averaged client values of repeated spots in a probe O
32. Probe Table Probe Correlation Figure 2 29 Selecting Array Results t Array Result Table onco a c ary m x Indes Label Type Master Marmalized Bkg Client Marmalized Bkg Ratio Normalized Bkg Expr 1 O8401 4 L spes e p T apama Ja 0 A 6 d4jmana 5 0 7 A 23 spmada ta 0 0 c 0 7 6 gjpmamb a A y y y o Fama 33 5 o0 A 0 ejams Eme y spmamb fae A y y y oa tojoraota a A y Mjmana pof A 34 q2mamb 5 o A 14 jamg JBude A y o MjOANa Bs 0 0 A 24 EU COM O NIE Figure 2 30 Array Result Table Example Using Array Compare 29 Data Description The possible columns of the Array Result Table are the following Table 2 1 Columns Index Label Type Master data Client data Master Quality Client Quality Result Expression Row Index Column Index Row 1 Row 2 Row 3 Columns in Array Result Table Short Description Running number Label of each spot in the array Type of spot empty guide reference background Chosen comparison data of master array Chosen comparison data of client array Quality flag of master array dots read from the Quality column of the master array s Array Metrix Array Result Table indicates artefacts automatically or manua
33. ackup when things go wrong Enter the autosaving time interval in minutes If you specify 0 minutes no backup will be performed autosaving Ed Autasave data temporary every BE minutes Cancel Figure 2 12 Autosaving Dialog Box View Menu view Window Help Images Quantil Plat Array Result Table Array Correlation Schematic Displav Schematic Histagram Analysis Table Probe Table Probe Correlation Figure 2 13 View Menu From the View menu you can select different data windows available in Array Compare 18 AIDA Array Compare User s Manual Window Menu Window Help Zoom All Fit Window Cascade Tile Horizontal Vertical Arrange Icons Close Close All wv 1 E Program Files raytest 4ida Image Analyzer deyv 3 10 028 Examplesjonco_a_c ary Figure 2 14 Window Menu Select the Zoom All option from the Window menu to fit the image to the manually changed window frame size To fit the frame size to the actual image size choose Fit Window The other options in this menu are standard Windows options described in the Windows manual Using Array Compare 19 raytest Toolbox Control Menu an lanas inmnarisnn Restore Window Position Save Window Position Automatic Restore Load Configuration Save Configuration Close Figure 2 15 Toolbox Control Menu Example Every toolbox has a hidden control menu attached which you can access by clicking on the title icon
34. actor in percent in the spin box located directly below the Automatic Size radio button In the Print section the Parameter checkbox enables the printing of the data and comment which are found in the File Information dialog box Check Overlays if you want to print the images with the array overlays superimposed on them Selecting Grayscale prints a bar next to the image showing the representation of various signal intensities as gray scales in the way they were set for the image Scales prints a bar next to the image that shows the length representation in the image 70 AIDA Array Compare User 5 Manual Print Options for Quantile Plot The Quantile Plot button on the Protocol Print toolbar allows you to configure the layout setting for the Quantile Plot window You can select the paper orientation Portrait or Landscape by clicking the appropriate radio button in the Format section The Graphic option in the Print section enables or suppresses the print output of the graphic displayed in the Quantile Plot window Protocal Print AS amp Print Preview Quantil Plot Format Portrait C Landscape Figure 2 90 Quantile Plot Print Options Using Array Compare 71 Print Options for Array Correlation The Array Correlation button on the Protocol Print toolbar allows you to configure the layout setting for the Array Correlation window You can select the paper orientation Portrait or Landscape by clicking the approp
35. anel on the Array Schematic toolbox you can configure the Schematic Histogram and the Schematic Display window to display certain ranges of data values in different colors ml Schematic Histogram onco_a_C ary z ri x Schematic Display Ratio of Marmalized Bkg Data H X n Colors JE 200 Counts 100 200 100 200 Log Ratio of Normalized Bkg Figure 2 56 Defining Color Coding Scheme For a more detailed view of the histogram the Schematic Histogram window provides a zoom function similar to the one provided by the Array Correlation window see the Array Correlation Window section for a detailed description of how to use the zoom function 46 AIDA Array Compare User 5 Manual Shortcut Menu of the Schematic Histogram Window The shortcut menu of the Schematic Histogram window provides one option Scales ry Schematic Histogram onco_a_cC ary oj x Zt k Scales Counts 200 200 100 D Log Ratio of Normalized Bkg Figure 2 57 Schematic Histogram Window Shortcut Menu The Scales option allows you to configure the graphical output After selecting the Scales option the Date Scaling dialog box opens Data Scaling l X Log Ratio af Marmalized Bkg tae Minimurn Maxirurn 200 Cancel i Automatic Counts Minimum Maximum 530 M Logarithmic v Automatic Figure 2 58 Data Scaling Dialog Box Using Array Compare 47 Here the
36. ard mode Two Pages Display Mode displays two pages at the same time One Page Display Mode displays one pages at a time Forward Button browsing navigation Back Button browsing navigation Figure 2 100 Toolbar of the Preview Window 80 AIDA Array Compare User 5 Manual Export and Import In AIDA Array Compare array comparisons as well as the content of all windows can be exported to a specific file Exporting Images To export the content of the Images window in a raster graphic format choose the Images option from the Export cascading menu of the File menu or select Copy Content from the Edit menu The Images Export dialog box opens asking you to specify a name and data format Windows Bitmap or CompuServe GIF format for the image export file After you confirmed the export by clicking the Save button the Image Export Options dialog box appears allowing you to set further option for the image file export Image Export Options X UK ES jm E Cancel Ea Height Te ecm E em whole image overlays underlay white Figure 2 101 Image Export Options Dialog Box Depending on the purpose of the export bitmap you can select the size and resolution of the resulting bitmap The raster graphic is exported in the Windows Bitmap or the CompuServe GIF format Note that the two images are exported as one overlaid image Use AIDA Image Analyzer to export each of the two images separately E
37. arry on using it DA Array Compare Aida Array Compare The evaluation time far the Aida software has expired Please call you vendor for a full Aida installation Copyrig ub OUL raytest lsotopenmekger te GmbH www ravtest de Figure 1 2 License Expired Message Box On purchase you get the program CD containing the purchased AIDA application modules together with a dongle hardware key see above and a permanent license number required to unlock the software Introduction 7 Problems Some problems might arise during the use of AIDA Please check first if your computer system is running smooth with regular software like word processors or graphical programs If the problems continue though other software runs fine we would like to know about your problems Please report the problem together with your hard and software settings to raytest so that we will be able to fix it in the next update of the program 8 AIDA Array Compare User 5 Manual Using Array Compare Program Structure The AIDA Array Compare program is a typical Windows program All standard Windows functions like moving and re sizing windows clicking buttons and using toolboxes are exactly as described in the Windows manual To keep this manual short all functions that are generally used by Windows programs are not explained in detail This manual assumes that you are familiar with Windows The term clicking always implies the use of the le
38. art of the array template definition procedure done in Array Metrix Nevertheless you can add additional information or replace existing information by importing them from external table sources using Array Compare s import name table options As in Array Metrix you can import up to four columns from a source name table In order to properly insert the rows of the source columns into matching row slots of the target table Array Result Table the position of the particular label column in the source table import table must be specified Array Metrix provides four methods for associating table rows 1 Import by Global Label 2 Import by Hierarchic Label 3 Import by Global Position 4 Import by Hierarchic Positions Using Array Compare 87 The Import by Global Label methods associates rows using the Label column Import by Hierarchic Label uses the Label 1 Label 2 Label 3 columns Import by Global Position utilizes the Row Index and Column Index columns whereas the Import by Hierarchic Positions method associates source and target rows via the Row 1 Row 2 Row 3 and Column 1 Column 2 Column 3 columns To import Name Tables to the Array Result Table 1 Click the Import menu item on the File menu and then choose Name Table from the cascading menu The Name Table Import dialog box appears 2 Select the file you want to import from the list of available files and click Open The file has to be in the Array Name Table or Table
39. ata of the master array are plotted on the x axis against the data of the client array on the y axis The mean of the Log ratios of the two arrays gray line and the data mean thresholds color coded lines configurable via the Array Schematic toolbox are represented see the Reviewing Array Comparison Data section for a more detailed description Using Array Compare 37 To open the Array Correlation window Select the Array Correlation option from the View menu view Window Help Images Quantil Plot Array Result Table Array Correlation kc Display Schematic Histogram Analysis Table Probe Table Probe Correlation Figure 2 42 Opening Array Correlation Window Correlation onco_a_c ary I O xl Client Mormalized Bk gq 95 D 1000 2000 S000 4000 s000 Master Normalized Bkg Figure 2 43 Array Correlation Window Example For a more detailed view of the plot the Array Correlation window provides a zoom function To zoom the correlation plot 1 Click the Selection tool on the main toolbar Esser Figure 2 44 Selection Tool on Main Toolbar 38 AIDA Array Compare User 5 Manual 2 Drag one of the axis with left mouse button pressed 3 Release the mouse button iBl x Client Mormalized Bk gq 95 400 1000 1200 1400 1600 1800 2000 Master Normalized Bkg Figure 2 45 Zooming Array Correlation Plot Alternative procedure 1 Click the Zoom tool on th
40. atio of Narmalized Bkg Data E 2 Colors JE 2 0000 B 2 0000 E Schematic Display Ratio of Mormalized Bkg Data E T Colors JE 0 Schematic Display onca a c ary Figure 3 15 Schematic Display Before and After Increasing the Expression Threshold Comparing Arrays 105 6 Review the comparison representations and data utilizing the data window interlinkage feature H Schematic Display onco_a_c ary i z ioj xj P 17 18 19 ai Array Result Table onco_a_c ary E e ioj x S lt Master 29 05A18a Correlation onco_a_c ary E ial x Correlation onco a c ary Client Normalized Bk g 95 Master Normalized Bkg Client Normalized Bk g Master Normalized Bkg 7 Figure 3 16 Reviewing Comparison Data and Representations 106 AIDA Array Compare User s Manual 7 Finally define two rules to include in the Analysis Table only those ratio values greater than or equal to 3 or smaller than or equal to 0 33 using the Filter panel of the Array Analysis Table toolbox EFA Array Analysis Table T Analysis Table onco_a_c ary E mi x Apply selected dots Index Label Type Ratio Normalised Bkg Expression Insert selected dots afer a ar San ue a0 pauco F7 emp sots bai ay ot Lens a ae a 121 0fAl2a Ifa 4 53 ES Filter darray Analysis Table Clauses Alternatives Clauses 1 Ratio Normalized Bkg gt
41. atios you can specify thresholds for the background range via the Cut Off and Parameter tabs All ratio values calculated from master and client values below these background thresholds will be processed using a special procedure described in the Reviewing Array Comparison Data chapter of this manual The default settings of the Cut Off tab provides you with a single Threshold spin box for specifying both the background threshold for the master and the background threshold for the client using a multiple of the standard deviation of the spots background values The default cut off threshold value is set to 3 standard deviations which has proved to be quite usable in the majority of cases Using Array Compare 57 The Parameter tab allows you to change the default settings for the threshold determination Just select the Explicit Threshold radio button and enter separate cut off threshold values for the master and the client on the Cut Off tab if you select explicit Threshold the appearance of the Cut separate cut off values for the master Off tab changes revealing spin boxes for specifying and the client Ratio Comparison Cut Off Farameter has Ratio Ratio Cut Off by Bkg Deviation 100 Ratio Comparison Figure 2 71 Setting Explicit Threshold Cut Of Parameter Master Cut OFF A416 g Client Cut Off B4 02 g Setting a Max Ratio value the highest ratio value possible can be very
42. ay comparison templates and reports printing images and results reviewing image information and exiting the program With the exception of the import and export functions it handles the entire data set of an image at the same time File Edit Evaluation Options wiew Window E Open Strg O Save Strg 5 Save 45 Close Import id Export Print Print Preview Printer Setup Information 1 etl Examplesjonco_a_c ary Exit Figure 2 4 File Menu New is used to create a new comparison between arrays You can compare two arrays if both were previously evaluated within AIDA Array Metrix The evaluation information is stored as mentioned above in an AIDA Data Format adf file To be comparable the arrays must be identical in number and order of the dots Click the Open option on the File menu to open an existing array comparison file Select the file you want to open from the list in the Open AIDA Data dialog box that appears The Save command is used to save the current comparison data Save As saves the active comparison with another path or filename Close closes the current images and comparison See the Options Menu section for a description how to set standard parameters for the default format and search path Import and Export allow you to exchange several evaluation data e g the export of the images with their overlays For a detailed description see the Export and Import section below Us
43. ay data except for the raw image data itself for comparison and saves it later together with the comparison results to the ary file so the array adf files becomes obsolete after saving your array comparison results To review the image and evaluation file information for the current data set select the Information option from the File menu File Edit Evaluation Options View Windoy Mew Open Strg O Save Strg 5 Save 45 Close Import d Export b Print Print Preview Printer Setup 1 et A Examplesyonca a c ary Exit Figure 2 1 Selecting Information Command from File Menu 10 AIDA Array Compare User s Manual This opens the File Information dialog box The File Information dialog box consists of three tabbed pages The Master Array tab displays all information stored in the ADF file of the master array This includes information about the image the underlying raw image data file the parameter file the measurement the device that created the image as well as information about the array evaluation file together with comments entered there The path of the files the date when the original image was created and the image resolution are shown For scanner images the image size resolution pixel size and depending on the data format of the image the file name originally used to store the scanned image are given However for camera images only the dynamic range and the resolution are gi
44. cal line on the right hand side the white threshold The actual values in this example 11372 and 65480 are also shown in the Black Threshold and White Threshold spin boxes on the Range panel of the Master Client Transfer control panel These values can be changed by moving the threshold indicators vertical lines in the histogram or by entering the values in the spin boxes The actual transfer curve is displayed between the threshold indicators in the histogram The transfer curve determines which original intensity x axis will be 60 AIDA Array Compare User 5 Manual represented by which intensity on the screen y axis The drop down menu directly below the histogram gives access to different transfer curves Quantum Level Gamma S Curve PSL The histogram s shortcut menu provides different views of the histogram window Full Reduced Enlarge Enlarge All The automatic or the full radio buttons can be selected to get automatic contrast enhancement or full scale representation respectively The Gamma value is used to change the incline of the Gamma and S Curve A Gamma value of gives rise to a linear transfer in these curve modes A value higher than 1 will enhance the representation of faint signals whereas a value below 1 will enhance the high intensity values Array Schematic Toolbox With the Array Schematic toolbox you can configure the settings for the schematic analysis of the array comparison 85 Array Schematic
45. d evaluation file adf as explained in the Data Structure section above Since AIDA Array Compare compares arrays previously evaluated within AIDA Array Metrix there is no need to create new overlay or edit existing ones Consequently AIDA Array Compare provides no functions for creating or editing overlays You can only select overlays to activate them When an evaluation is performed on the activated overlays the created data can be visualized in other windows like the Array Result Table window The data corresponding to activated overlays are highlighted in these windows Clicking beside an activated overlay or activating another overlay deactivates the previously activated overlay Its color changes to blue Clicking an overlay or dragging a frame with the left mouse button activates one or a group of overlays Main Menus When an file is open the following main menus are accessible File Edit Evaluation Options View Window Help Figure 2 3 Main Menu Note Many menu items can be directly activated through the corresponding button and connected toolbox in the toolbar see the Toolbar Structure section for details The Window and Help menu are general Windows features and will not be further explained So far no context sensitive help or tool tips are available 12 AIDA Array Compare User s Manual File Menu You use the File menu to perform general data transfer actions like creating loading saving and exporting arr
46. dOW c sarta aa ed P Ba Ra ARE V Pee Be es 49 Pata D OSCEIDITOI 2 0 zx ober ud tipa a A Ee TUR de CEU EAR SR 50 Probe Correlation MAIO rrara wx eb ees Gane SR OU e E deg RR UI rd 5 Toolboxes of Array Compare llleeleeeeee eee eee 53 Array Comparison Toolbox eeleeeeeeeeee es 54 Array Comparison Main Control Panel 0 0 0 0c eee ees 39 Normalization Control Panel 0 0 ee eens 56 Ratio Comparison Control Panel 0 20 00 00 eee 57 Display Control EOO DOX 46 onda cee aiden ARES eae Re R Ga SE e 59 Image Display Control Panel 0 20 0 000 eens 59 Master Client Transfer Control Panel 00000 cc ene 60 Array Schematic Toolbox 0 eee eee eee nes 61 Exclude From Schematic Section 65 06 000 nioni ni ene 62 ACMA Probe SECHONS seed eben eee teas eb ee ree Ne eS 63 Schematic Display Secon xs RP ESRUR pRSO PERO CAD HS CDSE SATAL 63 Array Analysis Table Toolbox 0 eens 65 Apply Selected Dots Section amp 4 4 xD XO EROR Re Ge Ga hae 65 Exclude From Analysis Table Section 0 000 000 ee eee eens 66 Inlet SCCUOM s iio ek RG aca ade Ea SENS Ree Reed ha wee Rei Qr s 66 iv AIDA Array Compare User s Manual Publishing Layout To0olboxs 3 4 45 6444 eddie RR este tea RE UE Print Options Tor Page Layout 3225 9 33 9 1p hone S tate get hee Print Options for Images Window osse ens Print Options for Ouanule Plot sise rr EEa
47. displayed in the Schematic Histogram window Protocol Print re Print Preview L Schematic Histogram Format f Portrait Landscape Print Iv Graphic Figure 2 93 Schematic Histogram Print Options 74 AIDA Array Compare User 5 Manual Print Options for Array Analysis Table Clicking the Array Analysis button switches to the layout setting controls for the Array Analysis Table window To select the paper orientation Portrait or Landscape click the appropriate radio button in the Format section In the Print section the scope for the print output can be specified To enable printing of the table check the Table box and specify the appropriate output extent using the Full Table Rows above radio buttons Protocol Print A Print Preview Analysis Table Format Portrait C Landscape f Full Table Rows above Figure 2 94 Array Analysis Table Print Options Using Array Compare 13 Dg b m S QU aS E S EE raytest Print Options for Probe Table Clicking the Probe Table button switches to the layout setting controls for the Probe Table window To select the paper orientation Portrait or Landscape click the appropriate radio button in the Format section In the Print section the scope for the print output can be specified To enable printing of the table check the Table box and specify the appropriate output extent using the Full Table Rows above radio buttons
48. e main toolbar BEJK Figure 2 46 Zoom Tool on the Main Toolbar 2 Draw a rectangle around the area of the plot you want to see in more detail Using Array Compare 39 Client Mormalized Bk gq 95 900 1000 1200 1400 1600 1800 2000 Master Normalized Bkg Figure 2 47 Zooming Array Correlation Plot Alternative Procedure To review the data value of dot pairs master client shown in the Array Correlation window click one of the respective dots The coordinates of the dot pair are highlighted together with all repetitions of the respective dots Client Mormalized Bk gq 95 1000 2000 S000 Master Normalized Bkg Figure 2 48 Reviewing Array Correlation Plot Values 40 AIDA Array Compare User 5 Manual Shortcut Menu of the Array Correlation Window The shortcut menu of the Array Correlation window provides two options Scales and Grid EE Correlation onco_a_c ary Bl x BOO 500 Ie scales a rid in T 4000 H T p4 E t D T 0 1000 2000 S000 4000 Sin Master Normalized Bkg Figure 2 49 Array Correlation Window Shortcut Menu The Scales option allows you to configure the graphical output After selecting the Scales option the Date Scaling dialog box opens x Master Mormalized Bkg 95 TOK Ok Minimum Maximum EE qz ow M Logarithmic v Automatic Cancel Client Marmalized Bkg 95 hinirurm haxirurm 59 al 669
49. eS s ONE n ee Master Cut DI 10 00 M bm e Bo s m aai n mud HEU E Client Cut O10 i Hutt o o o oc err on n o o g B B RR e Htt B HHHH 0808 08 8 80 eG M BRGIAM G IR amp M A 00 8 8 8 8 IHl f in we B ANGERS oe HW Be BAG BRGRGRBRO NB 0 RARO 0808008 0 ocR RBGBO 0 0 Mt c S EREE ae es E EERE E e Correlation onco_a_c ary lal x 1000 100 a i m 10 Ta H H E 1 m Z E Er 0 1 ta 0 01 0 001 0 01 0 1 1 10 100 1000 Master Normalized Bkg Figure 3 13 Schematic Display and Correlation Plot After Setting Background Threshold Comparing Arrays 103 Note that the number of colored dots in the Schematic Display window has considerably decreased 4 On the Array Schematic toolbox check the Exclude from schematic options for the dot types you want to exclude from the ratio comparison calculation and Schematic Display as well as from the Schematic Histogram and the Array Correlation plot H8 Schematic Display onco a c ary t Array Schematic 29 i Exclude fram schematic empty dots Y reference dots bad quality dots 9 Schematic Display anco a c ary l l e mi x Ze Figure 3 14 Excluding Dots 104 AIDA Array Compare User s Manual Se raytest 5 Increase the values for the expression thresholds via the data range spin boxes on the Schematic Display panel of the Array Schematic toolbox Schematic Display H Schematic Display onco a c ary R
50. ed Columns Decimal Delimiter f Point List Delimiter Tabulator C Comma System Defaults Figure 2 108 Analysis Table Export Options Dialog Box C Comma C Semicolon You can specify the Range of the exported rows and columns as well as the List Delimiter and Decimal Delimiter in the respective panels of the dialog box Complete the action by clicking the OK button The data are saved to a simple ASCII text file Exporting Probe Table To export the Probe Table On the File menu click the Export menu item and then select Probe Table from the cascading menu In the Probe Table Export dialog box that appears enter a name for the export file Using Array Compare 85 After you confirmed the export by clicking the Save button the Probe Table Export Options dialog box appears allowing you to set further option for the export of the probe table Probe Table Export Options E X Range Parameter W Table Header Cancel 6 All Rows Selected Rows Canel f All Columns t Selected Columns List Delimiter Decimal Delimiter Tabulator C Point f Comma C Comma C Semicolon System Defaults Figure 2 109 Analysis Table Export Options Dialog Box You can specify the Range of the exported rows and columns as well as the List Delimiter and Decimal Delimiter in the respective panels of the dialog box Complete the action by clicking the OK button The data are saved to a simple
51. ed from the drop down menu of the Array Comparison toolbox s Normalization section Mormalisation Global Reference Dots xd i No Reference E w Global Reference Dots M Grid Reference Dots Data Range Figure 3 6 Normalization Method Drop Down Menu After the normalization process is completed additional columns Normalized 9 o Normalized Bkg Reference Reference Bkg are inserted in the Array Result Table For details about this columns see the Array Result Table Window section of this user s manual Global Reference Dots Marmalisatian Global Reference Dots Normalization Method Drop Down Menu Reference Dot Selection Tool as Sec Unref Button Reference Dot Deselection Tool pu c Ref Button Markby Color Label Figure 3 7 Reference Definition Section Overview Each result integral or integral minus background of a spot is referred to either the mean value of all spots or to individually selected normalization spots Normalization is done using the same reference or reference bkg value for all spots 96 AIDA Array Compare User 5 Manual To mark a reference spot normalization spot 1 2 3 2 Choose the Selection tool from the main toolbar Click the designated spot Click the Ref button below the drop down menu in the Normalization panel Alternative procedure Activate the reference dot definition mode by clicking the Reference Dot Selection tool on t
52. el mport by Global La A Tahi Import by Global Position Import by Hierachic Label Mat Import by Hierarchic Positions Link Figure 2 113 Selecting Import Method Using Array Compare 89 5 Specify the associations between source table name table to be imported and target table current Array Result table depending on the import method you selected If you specified the Import by Global Label method or the Import by Hierarchic Label method Specify the position of the label column in the source table using the Label Column spin box for Import by Global Label or the 1 Level Label 2 Level Label Spot Label spin boxes for Import by Hierarchic Label Import Name Table onco a c ary Delimiter lt TAB Li Delimiter a E mm Figure 2 114 Specifying Label Column Positions If you choose the Import by Global Position method or Import by Hierarchic Positions by Hierarchic Positions is selected Import Name Table onco a c ary Delimiter lt TAB Li Delimiter Ct Te Column Index 1 Level Row Index 2 E Lii 7 Level E Spot Level Figure 2 115 Specifying Index Positions 90 AIDA Array Compare User 5 Manual 1 Level Label e Label Column EE 2 Level Label Spot Label sage i n Import Name Table onco a c ary Li a mm Specify the positions of the column and row indices in the source table using the Column Index and
53. ence dots The values of these dots are then used for normalization calculations Normalisation Reference Method Normalisation Drop Down Menu Global Reference Dots Reference Dot Selection Tool Global Reference Dots Y Reference Dot Deselection Tool N F ie ret o Reference ret Kap pe Unref Button E Ref Button wv Global Reference Dots Markby Color Label M Grid Reference Dots Data Range Figure 2 69 Reference Definition Section Overview For details see the Normalization section of this manual 56 AIDA Array Compare User 5 Manual Ratio Comparison Control Panel The Ratio Comparison control panel provides options for calculating the ratios of selected data Ratio Comparison Ratio Comparison Cut Off Parameter Cut Off Parameter Threshold 3 StdD ev g Max Ratio 100 Ratio Cut Off C explicit Threshold by Bkg Deviation Figure 2 70 Ratio Comparison Control Panel left Cut Off Tab right Parameter Tab Calculating ratios of data values within background range results in biased expression values since all measured data values exhibit a certain amount of random error due to the inherent bias of the cloning filter production filter processing spotting and scanning procedures Therefore values within background range oscillate around 0 Forming ratios using those biased background range values just yields results comprised entirely of biases To filter such biased r
54. ft mouse button The use of the right mouse button will be explicitly mentioned For multiple selections first click an item then hold down the Shift key while selecting another one to ensure that all items between those two in the list are selected To select two or more non adjacent items click an item then click another one while holding down the Ctrl key Holding down the Ctrl key and clicking an item a second time will deselect it Menus and toolbars allow a user to interact with the AIDA program Most functions are accessible by clicking the appropriate button on the toolbar as well as by clicking the appropriate item on a menu Both the toolbar and the menu change depending on the active window and toolbox within the AIDA program Functions activated by buttons from the toolbar or from menus always affect the currently active window You can distinguish the active window from the inactive ones by the different color of the title bar Just click on the desired window to make it active Current messages are displayed in the status bar at the bottom of the screen The appearance of the status bar also depends on the active window AIDA Array Compare is a modular program In the Evaluation menu you can choose from the available functions whereas the basic functionality is build into the integrating software Whenever you switch from one evaluation to a another one the results of the actual evaluation will be stored in the Array Data
55. he Normalization panel Then select a spot in the Images window To remove a previously assigned reference flag from a spot 1 2 Click the spot s you want the reference flag to be removed Click the Unref button on the Reference Definition panel Alternative procedure Click the Reference Dot Deselection tool on the Normalization panel Then select the spot in the Images window you want the reference flag to be removed Reference spots can by marked by color or label Just specify the marking by selecting one of the Mark by radio buttons Grid Reference Dots Using the Grid Reference Dots method each sub grid is normalized individually The reference value for a sub grid results from averaging the integral or integral bkg values of all reference spots in the sub grid Comparing Arrays 97 Data Range Data Range represents an additional normalization method where guide dots empty dots and dots with low high signal intensity can be excluded from referencing Mormalisation Data Range ig Master Client Ignore Upper 5 0 Ignore Lower 5 0 v exclude quide dots Iv exclude empty dots Figure 3 8 Data Range Normalization Method Only the mid data ranges of the arrays are used for normalization purpose These ranges are displayed in the Quantil Plot data view Data Range is a global normalization method normalizing all spots using the same reference value Setting up and Reviewing Array Comparison
56. idden columns using the Select Columns option see below To specify the decimal digits for the value output in a column choose Setting of from the shortcut menu and enter the value for the decimal digits in the dialog box that appears rm Array Result Table onco a c ary mi x Index Type Label Master Integral Area Client Integral Area Ratio Integral rea A S5nrt ascending by Master Integral Area 1 8a 0840 Sort descending by Master Integral 4rea wl oao mM Select Master Integrall rea 3fsa fon 11 Hide Master IntegrallArea OSA iis of Master Integral Area 1 1 S One lined Header Select Columns BlEmpyjaote S 3J amp Joo oa nc 1n17 P7 01 pum OK Cancel Figure 2 38 Specifying Decimal Digits Display Using Array Compare 35 Note that the behavior of the Settings of option depends on the column you perform the right click Columns whose cell contents is usually provided via name table import 1 e the Name and the ID column as well as the two user definable columns with the default name lt unused gt have Column Settings dialog boxes totally different from the ones provided by measurement value output columns Column Settings Name X iets eerie bine PO Enter here the whole URL link to an internal or external database Place a 61 atthe position where the cell value is ta be expanded in OK Cancel the URL query Figure 2 3
57. in the upper left corner of the toolbox You can use the toolbox control menu to restore Restore Window Position or save Save Window Position the position of the data windows In addition the configuration can be loaded from or saved to the scheme you saved using the Preferences option of the Options menu Just click on the Load Configuration or Save Configuration menu item respectively Toolbar Structure When you start AIDA Array Compare the following toolbar is displayed Figure 2 16 Toolbar on Program Startup On opening an array file please follow the instructions in the Tutorial the toolbar will change its appearance so that all visible functions are accessible iS a e E valuation ER Figure 2 17 Toolbar on File Opening Clicking an icon activates a function that in most cases can also be accessed through the menus or from the toolbox Some functions open a toolbox whereas others initiate a function that will be activated by one or multiple mouse clicks 20 AIDA Array Compare User s Manual File Options left section These function are also found in the File menu and are explained in the respective section of this manual These functions will always effect the image and entire data set of the active window nle alee Preview Button Print Button Export Evaluation Results Button View Result Table Button Save Button Open Button New Button Figure 2 18 Toolbar Left Secti
58. ing Array Compare 13 The Print command allows you to print your image and results data on the fly without permanently storing the layout printing settings whereas the Protocol Print panel provides you with a complete set of printing features which includes saving the settings with the data file for reasons of reproducibility Printer Setup opens the standard Windows Printer Setup dialog box for your printer The Print Preview option shows the appearance of the currently configured printout multiple pages on the screen For a detailed description of all print functions see the respective sections below The Information item as already described in the Data Structure section above displays a dialog box with resolution and size information of the current image file the current evaluation type the date of the last changes and other available evaluations Edit Menu The options in the Edit menu are related to the current window Their availability and specific actions depend on the active image or data window and the active overlays Edit Evaluation Op Copy Content faut Gop Paste Delete Unselect Select All Figure 2 5 Edit Menu Copy Content copies the content of the active data window into the clipboard using an appropriate data format See the Export and Import section for the available options for exporting the image to the clipboard in the Windows bitmap format Usually Cut Copy Paste and Delete are
59. interest within a specified range are displayed in one of the colors DATA X option or the deviation to the mean value is coded by the colors MEAN SD option If the DATA X option is selected you can set the data range for each color by dragging the border of the respective color bar in the miniaturized Schematic Histogram with the mouse or by entering the explicit values into the data range spin boxes If the MEAN SD option is selected this feature is disabled Instead the deviation of the spots to the mean value of the Log ratio data is given in units of 10 standard deviation SD of Log ratio Enter the step size in the SD Pitch spin box schematic Display schematic Display Fatio of Integral Fatio of Integral Data Hx F Colors 7i Mean 50 Colors 7i sp Piten T E 8 0000 E 3 430 1 7118 4 0000 B 2 0 1 4304 gt 1 0 1 1952 20000 E 9887 d 20000 8 3 0 3 1983 4 0000 E 2 0 1 4342 3 0 1 7164 5 0000 B Figure 2 80 Setting Data Range left and Specifying Step Size right Note that all data range values have to be entered and are given in terms of expression values ratio values gt 1 are converted to expression values ratio value whereas ratio values lt 1 are converted to expression values 1 ratio value into the spin boxes For the ratio comparison of means the mean values of the Log ratio data given in units of 10 standard deviat
60. ion SD of Log ratio are shown adjacent to the respective expression values 64 AIDA Array Compare User 5 Manual Array Analysis Table Toolbox With the Array Analysis Table toolbox you can configure the settings for the Analysis Table window E Array Analysis Table Apply Selected Dots Insert selected dots Rar EEEE EEE Apply Selected Dots Section Clear applied attributes Exclude from Analysis Table Empty Dots Guide Dots Background Dote Exclude From Analysis Table Section Reference Dots Bad Quality Dots Filter Edit E o View Analysis Table View Analysis Table Table Figure 2 81 Array Analysis Table Toolbox Overview Apply Selected Dots Section The controls of this panel are used to manually add values to or remove values from the Analysis Table Apply selected dots Insert selected dots Remove selected dots lear applied attributes Figure 2 82 Apply Selected Dots Section Using Array Compare 65 Exclude From Analysis Table Section In the Exclude from analysis table section of the Array Analysis Table toolbox you can select some dot types for exclusion from the Analysis Table These types are empty dots guide dots and bad quality dots Exclude from Schematic Iv Empty Dots v Guide Dots Background Bots Reference Dots Iv Bad Quality Dots Figure 2 83 Exclude From Analysis Table Section Filter Section This panel allows you to guide
61. isplay onco 24 Hi A pl L H i rin eee E n F i ott i e e etete HI M DELL LI E pi 0 19898 H ett 00 C000 39 MO Get Er TA She p0 deco e e ev 0 sb Figure 2 53 Schematic Display Window Example 43 Using Array Compare Alternatively the deviation of the spots to the mean value of data of interest can be coded by color The display options for Schematic Display window are set using the Array Schematic toolbox see the respective section below for details of how to use the Array Schematic toolbox Because of the permanent linkage between all data windows you can use the Schematic Display window to easily navigate through the array on the Images window in order to select spots or spot groups IEE Schematic Display onco_a_c ary Figure 2 54 Interlinked Windows 44 AIDA Array Compare User 5 Manual Schematic Histogram Window This data window shows a graphical representation of the distribution of values for a given data type selected via the controls of the Schematic Display panel on the Array Schematic toolbox as displayed in the Schematic Display window mT Schematic Histogram onco_a_cC ary i mi x i t m a D 200 Log Ratio of Normalized Bkg 200 Figure 2 55 Schematic Histogram Window Example Using Array Compare 45 Using the Schematic Display p
62. kground corrected Integral divided by area of a spot Using Array Compare 3l Table 2 2 Data Types Data Type Short Explanation Integral Area Bkg Integral per area background corrected Normalized 96 Integral divided by the reference value Normalized Bkg Integral minus Background divided by reference E Array Comparison Master Array Onco_a adt over onco_a inf Data IntegralArea Integral Integral Bkg wv Integrall rea Integral Area Bkg Normalized Normalized Bkg Figure 2 31 Selecting Data Type Using Data Drop Down Menu Result depends on the mathematical operation selected from the second Data drop down menu of the Array Comparison toolbox see the respective section below which includes Ratio data and Difference data aan 22 Array comparison Master Array Onco_a adt over onco_a inf Data IntegralArea m ratia K difference w ratio Figure 2 32 Selecting Mathematical Data Operation 32 AIDA Array Compare User s Manual in Suess If one or several dots are selected in the Images window the corresponding rows in the Array Result Table are also highlighted and vice versa I ai Array Result Table onco_a_c ary E Master Integral Area PSL mmr Client Integral Area Ratio Integral Area PSL mmr Expression 10 074014 2 zADTb 13 401g Lopes je 8 E LR 15 0Dib 9 156 182 12 12 TjADe Emt 02
63. lient array are loaded to the master for comparison by clicking the Add button on the bottom of the control panel alternatively you can select Array Evaluation from the Import cascading menu of the File menu Although the comparison is done only between two arrays at a time up to four client arrays can be applied to the master array Scrolling through the client array list gives an impression of the behavior of a single dot position over the different arrays With the Remove button a selected client array is removed from the list The Data drop down menu allows you to select the type of data to be compared 22 Array Comparison Master Array Onco_a adf over onco_a int Data IntegralArea Integral Integral Bkg wv Integral 4rea Integral 4rea Bkg Normalized Normalized Bkg Figure 2 67 Data Drop Down Menu Using Array Compare 55 An additional drop down menu Math Operation drop down menu provides you with a selection of two different mathematical operations which can be performed in the comparison difference and ratio aan 22 Array comparison Master Array Onco_a adt over onco_a inf Data Integrali amp rea m ratia k difference w ratio Figure 2 68 Math Operation Drop Down Menu Normalization Control Panel For the comparability of the results of two arrays a normalization of an individual result set is necessary The Normalization control panel provides you with tools for defining refer
64. lly identified Quality flag of client array dots read from the Quality column of the client array s Array Metrix Array Result Table indicates artefacts automatically or manually identified Result of chosen comparison data Value of the Result column encoded according to the following scheme On result value of master within background range and client s result value above background Off result value of master above background and client s result value within background range Ratio ratio value gt 1 Ratio ratio value lt 1 Global grid position of a dot row component potential reference column for name table import Global grid position of a dot column component potential reference column for name table import Subgrid row position of the dot 1 level potential reference column for name table import Subgrid row position of the dot 2 level potential reference column for name table import Subgrid row position of the dot spot matrix level potential reference column for name table import where data denotes one of the following selectable from the Data drop down menu of the Array Comparison toolbox 30 AIDA Array Compare User 5 Manual Column Label 1 Column Label 2 Column Label 3 Name ID lt unused gt Table 2 1 Columns in Array Result Table Columns Short Description Column 1 Subgrid column position of the dot 1 level potential reference column for name table import
65. luation Menu Toolbar Correspondences Using Array Compare 53 Array Comparison Toolbox The Array Comparison toolbox allows you to control the comparison of arrays To display the Array Comparison toolbox On the main menu click Evaluation and then click Array Comparison Alternatively you can select the Array Comparison button on the toolbar 223 Array Comparison Master Array onco_c adf over onco_c inf Data Normalized Bkg ratio zu Array Comparison Main Control Panel onca a adfover Onco a inf Add Remove Normalisation Data Range bd Master client Ignore Upper 5 0 g Normalization Panel Ignore Lower 5 0 v exclude guide dots V exclude empty dots Ratio Comparison Cut Off Parameter Threshold 30 StdDev zl Ratio Comparison Panel Figure 2 65 Array Comparison Toolbox Overview 54 AIDA Array Compare User 5 Manual Array Comparison Main Control Panel Using the Array Comparison control panel you can specify the basic settings for comparing arrays 225 Array Comparison Master Array Onca a adfaoveronco a inf Data Mormalized Bkg Data Drop Down Menu ratio Math Operation Drop Down Menu Onca cadi over onca c inf Loaded Clients List Add Remove Figure 2 66 Array Comparison Main Control Panel Overview The upper part of the control panel displays the name of the master array file C
66. lumn to be displayed in the header of the imported column in the Table Header Name text box 8 Enter the query string for database search using database specific query syntax in the Link text box Alternatively you can select predefined previously defined query strings from a list a Click the button next to the Link text box The Table URL Links dialog box opens b Choose an entry from the list box and click OK Using Array Compare 9 Se Table URL Links Gene Bank http Aew ACHAT Ah gowentres guerntegi cmd search amp db Figure 2 117 Selecting Query String From the Table URL Links Dialog Box 92 AIDA Array Compare User s Manual Comparing Arrays Loading Master and Client Arrays To load two arrays for comparison 1 Choose New from the File menu The Array Evaluation Import dialog box appears allowing you to select an array comparison master file Array Evaluation Import noname i Look in a Examples t 2 Ag Eest adf se Clontech Large Array adf Fa Rat adf Onco a adf 28 Panls2 adf se Simple Array adf 28 Pools adf 2 Poolsic adf File name Dneo a adf Files af type ADA Data Format L ancel Figure 3 1 Loading Array Comparison Master File 2 Select the appropriate file and click Open 93 The array is loaded in the first half of the bipartite Images window and the file name is listed below the Master Array heading in the Array
67. mal Delimiter in the respective panels of the dialog box Complete the action by clicking the OK button The data are saved to a simple ASCII text file 82 AIDA Array Compare User s Manual Exporting Array Correlation To export the Array Correlation display On the File menu click the Export menu item and then select Array Correlation from the cascading menu In the Correlation Display Export dialog box that appears enter a name for the export file Correlation Display Export onco a c ary ajx Save in c Examples t et E runlength win Flename ococorelsion Save as type windows Metafile Cancel Figure 2 104 Correlation Display Export Dialog Box Complete the export action by clicking the Save button The data are saved to a file in the Windows Metafile format Exporting Schematic Display To export the Schematic Display On the File menu click the Export menu item and then select Schematic Display from the cascading menu In the Schematic Display Export dialog box that appears enter a name for the export file Schematic Display Export onco a c ary ajx Save in E Examples t c E an onco correlation wmf File name onco schematic display Save as type windows Metafile Cancel Figure 2 105 Schematic Display Export dialog box Using Array Compare 83 Complete the export action by clicking the Save button The data are saved to a file in the
68. nd Overlaid Display buttons correspond to the Tile Horizontal Tile Vertical and Overlaid Display options of the Images window s shortcut menu see Shortcut Menu of the Images Window section above As mentioned in the Shortcut Menu of the Images Window section the non overlaid display types use grayscale for displaying the images whereas the Overlaid Display option shows the two Using Array Compare 59 Dg b m S QU aS E S e raytest images superimposed on each other in false color display In addition if the Overlaid Display option is active you can choose to display the images in inverted false colors which is recommended for print outs Just check the Inverted option Master Client Transfer Control Panel The transfer for the master and the client images are adjustable separately To switch between the transfer setting for master and client array click the appropriate tab on the Master Client Transfer control panel ape I Client TE Master Hes Transfer Transfer Quantum level is Black Threshold Spin Box White Threshold Spin Box Figure 2 74 Master Client Transfer Control Panel Left Master Tab Right Client Tab The histogram provided on the Master Client Transfer control panel 1s a representation of the number of pixels y axis that have the same intensity x axis The vertical line on the left hand side of the histogram represents the black threshold the verti
69. nly good repetitions are used for the calculation of the averaged values To display the Probe Table window select Probe Table from the View menu view Window Help Images Quantil Plat Array Result Table Array Correlation Schematic Displav Schematic Histagram Analysis Table Nx Correlation Figure 2 60 Selecting Probe Table View Bi Probe Table Compare nca a amp c ary 3 E B x Index Repeated Mame ID Master Good Client Good Master Mormalized Bkg C Gg5 GI gs 413 4 ec 3E ow a 2 2 2 qTB563 5 cmd 1 2 ee 8 eme 2 2 oml 5 aA 1 3 223 8 2iew n FN TPP 144 3 2 J 2a 2 sme 1 2Mvr amp jwQ 2 2 T ta 2jERB amp EG o T o 1978 na k Tum aan jn ER NNNM Figure 2 61 Probe Table Window Example Using Array Compare 49 Data Description The possible columns of the Probe Table are the following Table 2 3 Probe Table Columns Column Index Repeated Master Good Client Good Master data Client data Ratio data Expression Name ID lt not used gt Short Description Running number Number of repetitions of the probe in the array as determined by the spotting pattern Number of repetitions in the master array not flagged for Bad quality Number of repetitions in the client array not flagged for Bad quality Selected master ar
70. on Overview The New Open Safe Print and Print Preview buttons open the respective dialog boxes explained in the File Menu Print and Preview View Result Table opens the Array Result Table window for details see the respective section below Clicking the Export Evaluation Results opens a dialog box for specifying a file name and path for the export file see the Export and Import section for details Visual Tools middle section This part of the toolbar contains all mouse driven tools that can be activated at any time for any window such as images tables and graphs some restrictions apply Additional buttons may come up when certain toolboxes are or were open and are covered in respective toolbox sections Eyedropper Tool Move Tool Zoom Tool Selection Tool Figure 2 19 Toolbar Middle Section Overview You can use the Select tool to pick activate select dots in the windows for evaluation The selected dot will turn magenta To select more than one dot press down the Ctrl key and click on the desired dots subsequently You can also open a rectangle by clicking the position for the designated upper left corner of the rectangle holding down the mouse button and pulling to the designated lower right corner of the desired area All objects in the covered area will now be selected magenta You can deselect single objects by holding the Ctrl key and clicking them a second time Using Array Compare 21 Note that in A
71. onfigure the printout to contain only the overlays results and graphs that are currently needed Print Array Compare Compare Onco_a tc ary E E X Printer Kyocera Mita FS 1010 EX at Mar JK v Parameter Parameter and Image Options Iv Images whole image V overlays Iw Guantil Plot portrait M grayscale Iv Array Correlation Iv scales automatic size M Schematic Display M Schematic Histogram M Analysis Table M Probe Table W Probe Correlation Schematic Display Options portrait d Analysis Table Options portrait i i full table C rows above Probe Table Options portrait i i full table C rows above Figure 2 97 Print Array Metrix Dialog Box Click the check boxes for the various items to enable or disable them Select the number of copies you want to print 78 AIDA Array Compare User 5 Manual The margins of the printout can be selected in the Edges part of the dialog box The Header button opens the following dialog box Page Header and Footer X Header Iv file path M page number i current date Footnote M author M last change time M software version Figure 2 98 Page Header and Footer Dialog Box Here the Header and Footer of the report can be configured to contain various image and evaluation specific data The Parameter data overlays the Images Array Correlation Schematic Display
72. oving the pointer horizontally with the left mouse button pressed However in the built in Array Compare mode this function is similar to the selection function accessed by clicking the arrow button explained above Using Array Compare 23 Evaluation Option right section first half Clicking the Evaluation button opens the Change Evaluation Mode dialog box Evaluation 33 DEI IAI 3I 5 Available Evaluation Modes Cancel Figure 2 22 Changing Evaluation Mode In the Change Evaluation Mode dialog box you can choose an evaluation mode from the Available Evaluation Modes list The content of this list reflects the installed AIDA modules If no module is installed only the Array Compare mode entry is displayed Toolbox functions right section second half The buttons on this part of the toolbar are used to open the various Array Compare toolboxes For further description see the Array Compare Toolboxes section below Shortcut Menus Shortcut menus are attached to all data windows and the image They enable a comprehensive functionality without overcrowding the desktop The menus can be accessed by right clicking on an item in a window The menus offer functions related to the configuration of the clicked item Most of the time these functions are not vital for a successful evaluation however they will help to optimize the configuration of the output based on personal needs The settings in these men
73. ray probe value average of the Good dots values Selected client array probe value average of the Good dots values Ratio between Master data and Client data Ratio data value encoded according to the following scheme On value of master within background range and client s value above background Off value of master above background and client s value within background range Ratio ratio value gt 1 1 Ratio ratio value lt 1 Name of the probe corresponds to the Name column of the Array Result Table ID of the probe corresponds to the ID column of the Array Result Table User definable columns corresponds to the respective columns of the Array Result Table where data denotes one of the following selectable from the Data drop down menu of the Array Comparison toolbox 50 AIDA Array Compare User 5 Manual Table 2 4 Data Types Data Type Integral Integral Bkg Integral Area Integral Area Bkg Normalized 96 Normalized Bkg 96 Short Explanation Integrated raw intensity of a spot Integral background corrected Integral divided by area of a spot Integral per area background corrected Integral divided by the reference value Integral minus Background divided by reference Probe Correlation Window In the Probe Correlation window the probe data of the master array are plotted on the x axis against the probe data of the client array on the y axis The mean
74. riate radio button in the Format section The Graphic option in the Print section enables or suppresses the print output of the graphic displayed in the Array Correlation window Protocal Print re amp Print Preview amp Array Correlation Format Portrait C Landscape Print v Graphic Figure 2 91 Array Correlation Print Options 74 AIDA Array Compare User 5 Manual Print Options for Schematic Display To configure the layout setting for the Schematic Display window choose the Schematic Display button provided by the Protocol Print toolbar As for Array Correlation you can select the paper orientation Portrait or Landscape by clicking the appropriate radio button in the Format section The only option in the Print section Graphic enables or suppresses the print output of the Schematic Display window Protocal Print re amp Print Preview ee Bchematic Display Format Portrait Landscape Print L Graphic Figure 2 92 Schematic Display Print Options Using Array Compare 73 Print Options for Schematic Histogram The Schematic Histogram button on the Protocol Print toolbar allows you to configure the layout setting for the Schematic Histogram window You can select the paper orientation Portrait or Landscape by clicking the appropriate radio button in the Format section The Graphic option in the Print section enables or disables the print output of the graphic
75. s In order to achieve meaningful comparison data the settings for the background threshold using the Ratio Comparison panel on the Array Comparison toolbox and expression thresholds data range spin boxes on the Schematic Display panel of the Array Schematic toolbox have to be made properly Usually you will review the statistics of the array comparison using the correlation plot displayed in the Array Correlation window In the correlation plot the vertical and horizontal yellow lines indicate the background thresholds vertical line Master Cut Off horizontal line Client Cut Off whereas the lines shown in non yellow colors indicate the respective expression thresholds set by the data range spin boxes on the Schematic Display panel of the Array Schematic toolbox 98 AIDA Array Compare User 5 Manual Two diagonal yellow colored lines represent the Max Ratio value Max Ratio and 1 Max Ratio selectable via the Ratio Comparison panel of the Array Comparison toolbox Correlation onco_a_c ary 1000 100 Client Mormalized Bk g 0 1 0 01 0 001 0 01 0 1 1 10 Master Normalized Bkg schematic Display Ratio af Mormalized Bky Mean H 5D Colors JE SD Pitch 3 0 E 3 0 2 6034 1 0314 3 0 2 4474 1000 Ratio Comparison Cut Off Parameter Master Cut Off 10 00 Client Cut Oif 10 00 g Figure 3 9 Correlation Plot Representation of Comparison Parameter
76. ses f i z Integral FSL E a a E Analysis Table Clauses X Integral PSL BL cmn Figure 2 66 Specifying Rule Expression Using Array Compare 67 Publishing Layout Toolbox The Publishing Layout toolbox is used to configure the various print settings provided by Array Compare In contrast to the settings performed via the Print command of the File menu the Protocol Print options are permanently stored with the evaluation data A Publishing Layout left Protocol Print AD Print Preview n I PageLayuut Edges cm iD ul ce e Ooo Header v file path v page number DY current date w author v last change time v software version TEL lt Footnote EE _ it Te 5 Figure 2 87 Protocol Print Toolbar 68 Page Layout Button Images Button Quantile Plot Button Array Correlation Button Schematic Display Button Schematic Histogram Button Analysis Table Button Probe Table Button Probe Correlation Button AIDA Array Compare User 5 Manual Print Options for Page Layout Selecting the Page Layout button you can specify the layout for the printout Protocal Print Fe Print Preview 5 Page Layout Edges D n3 c a oo bottom 2 0crn T r2 m k NGG 4 Header Iv file path IY page number v current date
77. sion thresholds represented by the non yellow colored lines and determined by the data range spin box settings on the Schematic Display panel the real ratio values are calculated in any case This is due to the fact that small fluctuations in the measurement data causes large differences in interpretation especially at the intersection point of the Master Cut Off and the Client Cut Off For values which are within the range of the Max Ratio and Max Ratio thresholds the real ratio values are calculated and displayed in the Ratio column of the result table but the Expression value is set to On or Off By default the Threshold Cut Off value for both master and client is set in terms of multiplies of the Bkg deviation This behavior can be change by selecting explicit Threshold from the Parameter tab of the Ratio Comparison panel and then changing the threshold values for the master and the client separately 100 AIDA Array Compare User s Manual Max Ratio Client Normalized Bkg 1 Max Ratio 1 Master Normalized Bkg Figure 3 10 Correlation Plot Partitioned Into Different Ratio Calculation Areas Client Normalized Bkg 1 Master Normalized Bkg Figure 3 11 Correlation Plot Partitioned Into Different Expression Value Calculation Areas Comparing Arrays 101 Ratio Comparison Example Procedure 1 Load master and client array as described in the Loading Master and Client Arrays
78. talling AIDA Array Compare Follow these steps to install AIDA Array Compare 1 Insert the CD ROM in the CD ROM drive on your computer 2 Choose Run from the Windows Start menu to display the Run dialog box 3 Then type the following and click OK drive Aida Array Compare Setup exe where drive is the CD ROM drive identifier 4 The install wizard guides you through the installation process Click Next to proceed through the steps The Setup program installs the AIDA Array Compare program on your hard drive and creates a new group called Aida in the Windows Programs menu of your taskbar You can start AIDA Array Compare by selecting it from the Aida cascading menu Do not attempt to merely copy the files on the disk since this will not result in a successful installation of the program Note To execute AIDA Array Compare read and write permissions for the Aida Config folder must be set for all users Note The user s manuals are provided in Adobe PDF format To open the manuals from inside the program via the Help menu Adobe Acrobat Reader must be installed on your system If not please install Acrobat Reader A copy of Acrobat Reader is included with the installation CD in the folder Redistribution Acrobat Reader Dongle Protection Figure 1 1 Dongle Hardware Key 6 AIDA Array Compare User 5 Manual The full version of the AIDA software is protected by a dongle hardware key Before you can start the program
79. u EAE PP Print Options for Array Correlation 0 0 Print Options for Schematic Display llle Print Options for Schematic Histogram 0 0 00 c cece eens Print Options for Array Analysis Table 0 0 0 0 cee eee Print Options for Probe Table sa terrine nahi ne ea eens Print Options Tor Probe Correlation utr Sexo rre e EP ce wees BEXpott and Mpo i6 0c v ane op E deca dee wed ee e da o eeu cundo edenda dotes Expott tg MAGS ond oo e p EE tard teen eke loui drei i ebd Bbxport neOuanbile Plols eut area adt n d e d ach x et dub dd d Exporine Attay Results oscri esana herd cd Coed ews s want e Exporting Array Correlation iau dxaceg ia Edd Rap Edda ker a dr ROC Exporting Schematic Display isis tic tk Ye dahon tothe cede eA Shes ewes Exporting Schematic Histogram eS ex E eR eb n EA ERE Exporting Arnalysts D3ble ecco aa qo Cod d ote aee re S CREE Exporting Probe Table seers cione eia oa eh BO ed e E S o da dgedipeanid 8 aes Exporting Probe Correlation a ooa Eb eee Heb oou d edd eo Rd Importing Array Evaluations 0 0 ccc eee eee eee Importing Namo Tables vod np oad beta shiek adita c wapa ase eed Comparing Arrays Loading Master and Client Arrays 0 0 0 es INGEMALIZAN ON a3 Sess xen Bo hee Bees x etd We odo d aeta erigi ut eue d Global Reference Dots 0 ccc cece RR es Grid Reference DOotS sed 4h eet ooo s eee I RSU eed bw aw bbe uds atn MAST CDU otras ara
80. us can be saved using the Preferences command found in the Options menu Since shortcut menus are context sensitive they are explained together with the respective windows 24 AIDA Array Compare User s Manual l raytest Data Windows in Array Compare In Array Compare there are nine data windows available Images Quantil Plot Array Result Table Array Correlation e Schematic Display Schematic Histogram Analysis Table Probe Table Probe Correlation BE Aida Array Compare E 18 x File Edit Evaluation Options View Window Help Ioj xi schematic Histogram Com oi xi Eee eee Array Comparison Index Label Type Name Master Array onco_c adf over onco_c inf Data Normalized Bkg onco a adfover Onco_a inf 5676 08J12a 8a 5677 04 1284a ps3ind 5678 oaza aa 05 12a 10 100 1000 10000 Master Normalized Bkg 2 0 Add Remove Normalisation Data Range Master Client Ignore Upper 5 0 4 2ecwmogEV a b extracel E HE Boone TEE f j MV exclude guide dots Ooo 2 l i tise Ai AL LA 0 Se I exclude empty dots M o Ignore Lower 5 0 Ratio Comparison Cut Off Parameter Threshold 3 0 StdDev Client Normalized Bk g 95 Client Normalized Bk g 95 0 0101 1 10 10010010000 Master Normalized Bkg 3N51 BHK21 temperature sensitivity complementin 07J
81. used to edit overlays e g text and arrows placed in the image window or entries Since there is nothing to edit in AIDA Array Compare data windows these commands are disabled The Select All menu option selects all overlays present in the active image Unselect cancels all selections Options that are not available for the currently selected item will be displayed in gray as usual 14 AIDA Array Compare User s Manual Evaluation Menu Evaluation Options View la Array Comparison Display Contral Array Schematic w Array Analvsis Table Publishing Layout Figure 2 6 Evaluation Menu Selecting Array Comparison Display Control Array Schematic and Array Analysis Table or Publishing Layout opens toolboxes that are explained in the toolbar section below Options Menu Options View Window Hi Images Overlays Preferences Configuration Path Image Search Path Aubosaving Figure 2 7 Options Menu Various basic settings for current and future use of AIDA Array Compare can be made in the Options menu Selecting an item from the menu opens a dialog box where you can specify the settings Using Array Compare 15 The Images Overlays option is used to change the appearance of the overlays The options available in this dialog box depend on the image overlays defined in Array Metrix Image Overlays onco_a_C ary X E Array Overlay Label Array by 1 Level 2 Level Sind C
82. ven The dynamic range here 65536 gray scales and the total size of the image are displayed Information about the measurement and the device that created the image might be omitted if the device or image format does not support further exposure information File Information onco_a_c ary X Masher Array Client Array Evaluation Evaluation file Onco_a adt Evaluation date Wednesday Movember 15 2000 11 34 10 AM Parameter file g aPragram Filesiraytesti amp ida Image Analyzer dev 3 10 0281Examplestanca a inf Image data file B Program Filesiravtesti ida Image Analyzer dev 3 10 026 Examplesionco_a img Original file Og hzdla Scan date Wednesday March 28 2000 4 54 10 Pht Imaging plate type 23 40 Scanner Fuji FLA 3000 Sensitivity 4000 Latitude 5 Digital resolution 65536 16 bit per pixel Image size 230171529 115 05mm 75 145mm Pixel size 5 pm 5 um Comment d hlinks rechts 6 Tage exp Figure 2 2 File Information Dialog Box Master Array Tab On the Client Array tab the same type of information as for the master array are given for the client array The Evaluation tab contains information about the array comparison evaluation file ary Comments can be added for future reference Using Array Compare 11 Overlays Overlays are regions on the image as well as annotation defined within AIDA Image Analyzer and its modules They are saved together with other evaluation data in the associate
83. xporting Quantile Plots To export the Quantile Plot display On the File menu click the Export menu item and then select Quantile Plot from the cascading menu In the Quantile Plot Export dialog box that appears enter a name for the export file Complete the export action by clicking the Save button The data are saved to a file in the Windows Metafile format Using Array Compare 81 Exporting Array Results To export the Array Result Table On the File menu click the Export menu item and then select Array Results from the cascading menu In the Array Results Export dialog box that appears enter a name for the export file Array Results Export onco_a_cC ary xl Save in Cy Examples amp cf E3 File name demo tet Save as type Table ASCII File Cancel Figure 2 102 Array Results Export Dialog Box After you confirmed the export by clicking the Save button the Array Results Export Options dialog box appears allowing you to set further option for the export of the array results Array Results Export Options x Fange OK MW Header Cancel 6 All Rows Selected Rows Cancel AllColumns Selected Columns Decimal Delimiter f Point List Delimiter Tabulator C Comma System Defaults Figure 2 103 Array Results Export Options Dialog Box C Comma C Semicolon You can specify the Range of the exported rows and columns as well as the List Delimiter and Deci
84. y Compare User s Manual Consequently they are also excluded from the Schematic Histogram calculation and are not displayed in the Array Correlation plot Actual Probe Section In the message box below the Exclude from schematic section the name of the selected dot as stated in the Array Result Table is shown together with its label and the value for the measured data selected in the Data drop down menu of the Array Comparison toolbox Actual Probe Ratio Integral 1 0028 plasminogen activator inhibitor type Il Carginine serping PLANH2 Figure 2 78 Actual Dot Section Schematic Display Section The Schematic Display section is used to configure the display options for the Schematic Display window schematic Display Ratio of Integral Data Type Indicator Field Data HR 7 Colors JE Colors Spin Box Color Coding Drop Down Menu Miniaturized Schematic Histogram Data Range Spin Boxes Figure 2 79 Schematic Display Section Overview In the Data Type Indicator Field the data type to be displayed in the Schematic Display window is shown Using Array Compare 63 AN SS abt raytest To configure the color output of the Schematic Display window choose the number of colors 3 5 or 7 you want the data to be reduced to using the Colors spin box Specify the color coding scheme for the data via the drop down menu displayed to the left of the Colors spin box Either the data of
85. you have to plug the dongle into your parallel port If your printer cable is also attached to this port turn on the printer before starting AIDA This will avoid possible problems in recognizing the dongle by AIDA Other problems in recognizing the dongle can be caused by further dongles attached to your system In this case be sure that the AIDA dongle is the first one on port Since AIDA dongle is fully transparent it does not effect the other dongles Note that there is only one dongle for all AIDA products so there is no piling up of AIDA dongles at your parallel port Licensing Key If you have downloaded AIDA Array Compare from our website you need a license number to unlock the software When you install the software an hardware installation specific serial number is automatically generated If you start AIDA Array Compare the first time a dialog box appears asking you to enter your license number To get this licensing key you must register your AIDA copy by contacting the raytest customer service online or via phone FAX specifying the serial number given in the Serial text box of the License dialog box If you choose to register online complete and submit the web registration form You will get your licensing number via e mail within a few days The obtained license grants you a trail period of 30 days during which the software is full functional After the trial period has expired you have to purchase the software in order to c
86. yout toolbox However they are not stored with the data file Using Array Compare 79 The Preview option of the Publishing Layout toolbox allows you to preview all pages as configured in the Publishing Layout toolbox before they are actually printed Clicking the Preview button opens the Preview window directly since all layout setting are already made through the Protocol Print panel Hie Aida Array Compare Preview onco a c ary File Edit Evaluation Options View Window Help Py ele o Page 2 of 265 Page 3 of 255 Array Compare Wednesday Janay 23 2002 12 45 17 PM Array Compare Wednesday January 23 2002 12 45 17 PM EsProgram Files ways MAlda Image Analyzer dev 3 10 028 Example onco a cay modited Page 201265 EiProgram Fllez rayez l21da Image Analyzer dev 3 10 025 Example onco a cay modited Page 301265 Client Array Correlation Display vary Hoe ie d if T did EDT TS EC Ep li Lar I Changed Wednesday January 23 2002 12 44 14 Alda Amay Compare Development Version 3 20 020 Lar I Changed Wednesday January 23 2002 12 44 14 Alda Amay Compare Development Version 3 20 020 Figure 2 99 Preview Example The active zoom function allows to closely look at some details and works as described for the Zoom tool left mouse button zoom in right mouse button zoom out Besides the standard features the toolbar of the Preview window provides the following functions Close Button will return you to the stand

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