Melanie QSM 20022008.fm
Contents
1. Melanie 7 0 Quick Start Manual Edition AA 1 Melanie Quick Start 1 1 Launch the software 1 Inthe New Project window enter a Project Name and click OK New Project Enter New Project properties Project Name Bacteria Location C Documents and Settings Melanie User M Comment PCa 2 Inthe Open Files window locate and select the image files Click Open Open Files in Melanie Tutorial Files 21 A_T1_Gel1 mel 3B _T2_Gel3 mel B_T2_Gel3 mel A_T1_Gel1 mel A_T1_Ge All Image Files mel tif gel img i Gel Properties Gel Name 4_T1_Gell Staining Silver Apply Staining to All In the example every gel has the same stain therefore Apply 2 Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 Staining to All is selected to quickly load the images Workspace Menu bar Oo lbars Image Fool sheet File Edit View Reports Tools Help DA E S RAARO AA 2h Sh MN We AW Add Files to Project F Image Pool Ss w kz D a Gels 12 Spots 0 9 Annotations 0 Status bar The gel images are arranged in a tabbed sheet labelled Image Pool To open DIGE gels the file names must contain Cy2 Cy3 or Cy5 In the Create DIGE Gel window Melanie automatically recognizes and proposes the correct combination of DIGE images and the corresponding DIGE gel name2. Create DIGE Gel Select the images that are part of the same DIGE gel GelO1 Cy3Control Gel 01 CyS Treated Gel 02 Cy2 Standard Gel 02 Cy3 Treated Gel 02 Cy5 Control Gel 03 Cy2 Standard Gel 03 Cy3 Control Gel 03 Cy5 Treated Gel 04 Cy2 Standard Gel 04 Cy3 Treated Gel 04 Cy5 Control Once opened the two or three images in a DIGE gel are grouped in a pane within the Image Pool sheet Melanie 7 0 Quick Start Manual Edition AA 3 1 Melanie Quick Start 1 2 Customize toolbars 1 2 Customize toolbars The standard toolbars can be configured according to your individual specifications 1 To change the order click the left edge of a toolbar and drag the toolbar to the position you want File Edit View Reports Tools Help by PES i amp oo AA Sh Sh MN EE We A Add Files to Project The Image toolbar rotate flip invert etc is contextual i e it is only visible when there are gels in the Image Pool File Edit View Reports Tools Help bP 22 00 AA 2h Sho dN Pe A Add Fil s to Project 2 Toaddorremove buttons choose Tools gt Customize 3 Inthe Customize window under the Toolbars tab click New to create a toolbar Customize Toolbars Commands Keyboard Options Toolbars A Tools W Display Image C Edit Spots 4 Enter a Name for the toolbar e g Custom 1 Click OK 5 Click the Commands tab in the Customize window and select a category 6 Click the desired comman
3. File Edit View Reports Tools Help b P E RA O8 OGP4R AA 2h Sh dN Pe t Add Files to Project of TENE 4_T1_Gell 4_T1_Gel2 4_T1_Gel3 4_T2_Gell 4_T2_Gel2 4A_T2_Gel3 In the Workspace each of the open gel images is listed in the Image Pool The two or three images in a DIGE gel are grouped in a folder within the Image Pool folder To view details about the gel images click the Expanded View button in the Workspace toolbar To add more gel images right click on Image Pool and select Add The project name is also listed in the Workspace The Workspace shows the hierarchical structure of files gel images and folders projects match sets and classes Using the Workspace you can display copy paste move and rename files and folders 1 5 Create a hierarchical match structure It is recommended to use hierarchical match structures to compare your images i e find corresponding spots A DIGE gel is an inherent match set An example of a match hierarchy is shown below Melanie 7 0 Quick Start Manual Edition AA 7 Melanie Quick Start 1 5 Create a hierarchical match structure Gels or match sets with a red marker are used as the reference in viewing or matching and appear first in the list To change the reference drag the desired gel or match set onto the existing reference so that it moves into the first position Workspace Ow q Gr E Image Pool SBF Bacteria phy AB Cal Match 5 A pM AT
4. Files to Project button in the Image toolbar In the Add Files to Project window select a project and create a match set by selecting lt New gt In the Create MatchSet window enter a Name and click OK Add Files to Project Choose a destination project and matchSet Project v MatchSets In the example these steps were repeated to create four match sets ATl AT2 BT and BT2 Match sets can be further combined Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 5 Create a hierarchical match structure 3 Select the match sets e g AT and AT2 right click and choose Merge MatchSet Workspace Ow J J m F Image Pool S E Bacteria Display Create MatchSet E By Export MatchSet Copy Ctrl C Cut Ctrl X Paste Ctrl V rf Remove Del Properties B_T1_Gel2 B_T1_Gel3 L Classes S BT2 Gal Match B_T2 Gell B_T2 Gel2 B_T2 Gel3 C Classes 4 Inthe Create MatchSet window enter a Name and click OK In the example the match sets ATI and AT2 are merged into match set A BT and BI2 are merged into match set B Finally A and B are merged to create the root match set AB Root match sets contain the folders Match and Classes Workspace ai T 2 a F Image Pool SBF Bacteria S AB Match Ty E ATI H a AT2 S B H BT1 N H BT2 C Classes Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 5 To view the gels
5. I 4_T1_Gell A_T1_Gel2 A_T1_Gel3 pt AT2 A_T2 Gell A_T2 Gel2 A_T2 Gel3 Ca Classes When a DIGE gel is opened for the first time the reference image needs to be selected The Cy2 image is always proposed by default Bear in mind that not all gel images are matched equally Images from samples belonging to the same biological population or the same experimental group e g gels that have been run in the same batch are often easier to match Working with a hierarchical structure reduces the number of difficult matches e g AT versus AT2 or A versus B Furthermore only spots matched with a spot in another gel are included in Gel and Class Analysis Tables all soots are of course presented in a Spot Table The likelihood of a spot being matched is much higher when matching with a gel from the same biological population Spots that are represented in a single population such as a sub match set are therefore included in the analysis even if they are not in the global match reference 1 Select images e g A_T _Gell A_T1_Gel2 and A_T1_Gel3 in the Image Pool folder in the Workspace Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 2 Drag the images onto a project e g Bacteria In the Create MatchSet window enter a Name and click OK Create MatchSet Name Comment Alternatively 1 Select images e g A_T _Gell A_T _Gel2 and A_T1_Gel3 in the Image Pool sheet 2 Click the Add
6. Mean absolute deviation Half range size Classes for Statistical Tests ATI The Center i e mean value including 100 of spots is the default display in each class column The Max column lists the highest of these values You can also show the Dispersion for each class in the table or one of Melanie s Overlapping Measures between class intervals Class intervals are defined by the range Central value Dispersion Central value Dispersion These intervals are more easily understood when looking at the Class Analysis Histograms Melanie 7 0 Quick Start Manual Edition AA 21 Melanie Quick Start 1 12 Data analysis 22 Choose Reports gt Analyse Classes gt Histograms Class Analysis Histograms Mean 100 and M S D A By H B center v page 165 517 I 0 25 Sorted Values 02 v Adaptive Gradations abcdefzehijki 492 abedefzghijkl 493 abcedefzhijkl 494 Gell ATI _Gel2 ATI Gel3 AT 2 Gell AT2 A T2_Gel2 AT 2_Gel3 AT2 _Gell BT1 _Gel2 BT1 1_Gel3 BT1 2_Gell BT2 T2_Gel2 BT2 T2_Gel3 BT2 oe wj j be H RERI P e dae ara arm As en FN os Each histogram displays for a given spot the quantification values in the different gels as orange bars To see what gel corresponds to which letter click the Settings button in the histograms toolbar and select Show Labels Alternatively move your cursor over a letter
7. Melanie Quick Start 1 1 Melanie Quick Start Melanie is a comprehensive software for visualizing editing and analyzing two dimensional electrophoresis 2 DE data The goal of this introduction is to familiarize you with the new and improved interface It is the fastest way to start exploring and working with Melanie on your own More detailed and advanced information can be found in the User Manual We assume several things at this point e You are an experienced computer user e You have already successfully installed Melanie e You have knowledge of electrophoresis and staining techniques The image analysis workflow presented is idealized i e editing is not performed In reality gels offen need to be refined to optimize detection matching and ultimately the results The sample gels used in the examples study protein expression changes between four populations of gels Cells were grown under two different conditions substrate A and substrate B and underwent one of two treatments treatment 1 and treatment 2 Population Condition Treatment A_Tl Substrate A Treatment A_T2 Substrate A Treatment 2 B_TI Substrate B Treatment B_T2 Substrate B Treatment 2 1 1 Launch the software e Double click the Melanie 7 0 shortcut on your desktop e Click Start gt Programs gt Melanie 7 0 The first time you launch the software pop up windows prompt you to enter a name for a new project and to open the gels to be studied
8. all matched The two spots in gel B_T1_Gell are treated as a single entity in the quantification This means that their combined quantification values are compared to those of the spots in the other images To review matching choose Select gt Matches gt All and specify the hierarchical level at which you want to select the matches e g AB to select all soots matched to the global reference Matched spots are highlighted in green The matching of any red spots should be scrutinized However this can also be done during data analysis Melanie 7 0 Quick Start Manual Edition AA 17 1 Melanie Quick Start kll Create classes 1 11 Create classes In order to analyze gels or gel populations it is necessary to define classes A class is a set of gels or gel populations with common biological properties Comparing classes enables you to find the protein expression variations between different biological states Select a match set e g AT1 in the Match folder and drag it into the Classes folder In the Create Class window confirm or modify the Name of the class and click OK Alternatively Oo a A W ND In the Match folder select all gels to be added to a new class The gels may be part of different sub match sets but must belong to the same match hierarchy Right click and select Add in Class In the Add Gels in Class window enter a Name and click OK Repeat these steps until all classes are created Hold the S
9. button in the 3D View window includes features such as rotate Zoom and translate File Edit View Select Reports Tools Help AARS ORBICO ODALAR NO aAA TE AT1 AT2 BT1 BT2 aseds Hon BT2 Ratio gt 1 5 Validate 0 881418 1 30171 O m 0 870217 0 779136 I m 0 571771 1 17447 4 E 0 939756 0 198744 4 m E 0 668453 0 698166 X abedefghi jkl abedefzhi jk 0 832893 0 832893 0 832893 0 21058 J 212 214 0 808277 0 808277 0 808277 0 529469 4 0 701393 0 701393 0 691273 0 701393 4 Gels 12 Spots 12 Annotations 0 1 13 Export tables 1 To export a table in text Excel or XML formats for use in another software click Save in the table toolbar 2 Inthe Save Table window browse to the desired location and enter a File Name Click Save 1 14 Pick lists 1 To generate a pick list for a spot excision robot choose Select gt Spot Sets 2 Make a selection in the Select Spot Set window and click OK Melanie 7 0 Quick Start Manual Edition AA 25 Melanie Quick Start 1 14 Pick lists 3 Choose File gt Export gt Spots to Picker Consult the User Manual for more details about the different soot picker formats 26 Melanie 7 0 Quick Start Manual Edition AA
10. d in the list and drag it to the empty toolbar that was just created in Toolbars In the example a button Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 for Detect from the Edit category was added to the custom toolbar File Edit View Reports Tools Help WH APES RB OO AA 2h Sh AN Pe t Add Files to Project aceds OA Customize Toolbars Commands Keyboard Options o add a command to a toolbar select a category and drag the All Commands Built in Menus New Menu Gels 12 Spots0 Annotations 0 7 Repeat these steps to create a toolbar containing shortcuts to Commands such as Detect Edit Enabled Match Gels Add Match Delete Match and more 8 Close the Customize window 1 3 Work with gels The tools in the Image toolbar are convenient if gels need to be rotated flipped cropped or their gray levels need to be inverted AA Sh Sk dh SS We BW Add Files to Project The operations are only applied to selected gels To select a gel click the gel name Click the sheet tab to select all gels Use the Shift or Ctrl keys to select a subset of gels Melanie 7 0 Quick Start Manual Edition AA 1 Melanie Quick Start 1 3 Work with gels 1 3 1 Adjust the contrast 1 Click Magnify in the toolbar ra 2 Hold the Shift key and click in one of the images All images are zoomed with the same factor 3 Click Region in the toolbar i i 4 Hold the Shift key and defi
11. eName 4_T1_Gel3 Pixel Intensity 5096 i 254 408 Detect Spots 2 54 Parameters 4 08 214747906 205 Smooth Intensity 5104 Vol 4967 SRS A Zol Saliency Saliency 101 a i Yol Ratio L j Min Area Slope TaN i Auto Preview f Workspace _ Cursor Information pu Gels 12 Spots0 Annotations O 2 54 cm 4 08 cm 5096 Processing may take a few minutes to complete The detected spots are outlined in red Melanie 7 0 Quick Start Manual Edition AA 13 1 Melanie Quick Start 1 8 Add landmarks The DeCyder 2D co detection algorithm is applied to DIGE gels In the DIGE Spot Detection window enter an estimation of the Number of Spots present in each image Select Apply To All and click OK 1 8 Add landmarks To maximize the available space for viewing gels you can close the Cursor Information window and click Auto Hide to minimize the Workspace 1 Click Landmark in the toolbar 2 Position the cursor over a known well defined spot in the reference gel and click A Validated landmark symbol bold orange circle appears on the spot 3 Inthe other images drag the Non validated symbols green circle with orange plus sign onto the corresponding spots File Edit View Select Reports Tools Help HAR sO RB CO OGPB4R aseds pon Tues oo ie a a i LES DUFING POSITIONING AR 713 Gels 12 Spots 7 Annotations 7 4 4 cm 2 03 cm 5178 In certain gels the symb
12. etween any of the classes is now sorted in descending order 13 To select a spot in the gels click the relevant row in the table Melanie 7 0 Quick Start Manual Edition AA 23 1 Melanie Quick Start 1 12 Data analysis File Edit View Select Reports Tools Help 14 If the spot is expressed differently click Annotate in the main toolbar and enter a name for the Spot Set to be created e g Validate The box in the corresponding row is automatically checked AARS O RAICA ODALAR a AB ME AT1 AT2 BT1 BT2 aoeds HOA 1 25062 1 17447 0 987705 0 909563 0 903239 0 832893 0 808277 0 701393 Gels 12 Spots 12 Annotations 0 24 0 870217 0 571771 0 939756 0 909563 0 668453 0 832893 0 808277 0 701393 1 25062 0 770083 0 987705 0 909563 0 698166 0 832893 0 808277 0 691273 1 25062 1 17447 0 987704 0 472054 0 903239 0 631896 0 603082 0 404558 0 779136 1 17447 v 0 198744 IV 0 899175 I 0 903239 0 21058 0 529469 vj 0 701393 m igm igm jim jim jim im jia Ad O A X Gi Class Analysis Histograms Mean 100 and M 5 D Ovx 1x a a t F RE BR Center page 9 0 2 0 1 0 abedefzhi jki abedefzhi jkl 55 56 15 Use the up and down arrow keys to move to the previous or next row in the table Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 To look at 3D Views of spots choose Reports gt 3D View The Tools
13. hift or Ctrl key to select several classes To open the images in a classes sheet right click and select Display In the example the Classes defined reflect the structure in the Match folder This is not always the case in other experiments Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 File Edit View Select Reports Tools Help JP ERLO RB CO OGP R py AB MA AT1 AT2 BT1 BT2 gt Image Pool Bacteria p AB Upl Match phy A 2 4_T1_Gell 2B 4_T1_Gel2 Gels 12 SpotsO Annotations 0 You are now ready to create tables graphs and apply statistics to the spots gels annotations matches or classes All of these features are found in the Reports menu 1 12 Data analysis 1 To decide which quantification value to use for your analysis choose Tools gt Options 2 Inthe Quantification tab of the Options window specify the quantification values For non DIGE analyses the default is ZVol Melanie 7 0 Quick Start Manual Edition AA 19 1 Melanie Quick Start 1 12 Data analysis relative volume For DIGE analyses Vol Ratio is highly recommended Click OK Options Display Annotation Gel Descriptions Quantification Quantification ya vo DIGE Value Vol Ratio v Volume Quantification Compute area and volume in mm2 based on image resolution Differential analysis between populations of gels i e classes is essentially based on the values found in
14. imize the match vectors A blue upside down triangle on a spot indicates that the spot was matched to one or several spots in other gels for which no corresponding spot in the global match reference was found A spot with a triangle means that the corresponding position in the reference lies outside the visible area 1 10 Edit matches 1 Use the Select tool to click on a spot The spot and any matches are highlighted in green What can be done if all corresponding spots are not matched In the example the selected spot was correctly matched throughout match set A and within BT2 But due to spot splitting in gel B_T1_Gell it was not matched within match sets BTI and B File Edit View Select Reports Tools Help OAIR RB OB OG PBR w kz o fa amp Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 Rather than merging the two spots in B_T1_Gell spot edition should be avoided whenever possible the soots were both included in the match and treated as a single entity in the spot quantification 2 To add spots to a match hold the Shift or Ctrl keys and select all spots that should be part of the same match 3 Choose Edit gt Matches gt Add Match or click Add Match in the toolbar if present File Edit View Select Reports Tools Help i OAR 0 RA OO OGRA co wo v 9 O k Gels 12 Spots 13 Annotations 0 In the example the selected spots are now
15. in a match set in a new sheet right click on the match set name or images and select Display File Edit View Select Reports Tools Help OP ck o RB O08 OIRA Workspace a a Image Pool Ej E Bacteria foe Display Create MatchSet Merge MatchSet Export MatchSet Copy Ctrl C Cut Ctrl x Paste Ctrl V Remove Del Properties B_T1_Gel3 ph BT2 _T2_Gell _T2_Gel2 _T2_Gel3 al Classes Gels 12 SpotsO Annotations 0 The gels are placed in a sheet labelled with the match set name Gels in sub match sets are grouped in panes labelled with the sub match set name 1 6 Change layout You can change the layout of the Melanie interface in order to optimize the available space e To arrange your images use the buttons in the top right corners of the sheet or pane tabs Melanie 7 0 Quick Start Manual Edition AA 1 1 Melanie Quick Start laf 1 7 Detect spots To resize the Workspace drag its right border File Edit View Select Reports Tools Help OAS o RB OO OPARA a Image Pool i Bacteria B_T2_ B_T B_T2_ Cal Classes F Stacked E Tiled n E One Column HF Free 7 Oe er eS er 7 Gels 12 SpotsO Annotations 0 The Workspace is a dockable window i e it can either be attached to the interface window or be in a floating state Report windows are also dockable Detect spots To dock undock or close a dockable window u
16. mple 0 25 implies that 25 of the current class range is not recovered by one of the other classes In the same way a value of 1 5 implies that there is a gap equivalent to 50 of the current class range in comparison to the farthest other class Overlapping Measures enable you fo find significant protein expression Changes 6 Inthe Class Analysis Table click the Statistics drop down list to select Ratio 7 Click Select by Value in the table toolbar 8 Inthe Select by Value window specify all soots with a Max ratio greater than or equal to 1 5 Select By Value Match ID ax Match Count ATI Wilcoxon Kolmogorov mine 9 Click Annotate in the table tooloar and enter anew name for a Spot Set to be created e g Ratio gt 1 5 10 To limit the analysis to the currently selected spots choose Edit gt Active Spots gt Set Click the Select button in the main toolbars and then click anywhere in one of the images but not on a spot All spots are deselected The red spots are active and appear in reports tables histograms plots The yellow spots are inactive and therefore are not included in the reports To include or exclude spots from the active spot set select the spots in question and choose Edit gt Active Spots gt Add or Edit gt Active Spots gt Remove 11 In the Class Analysis Table click the Statistics drop down list to select Gap 12 Double click the Max column The maximum gap b
17. ne a region in one of the images A region of identical size appears in the other images 5 Click Contrast in the toolbar 6 To modify the contrast and brightness of the image and see the effect on the selected regions adjust the horizontal scroll bar below the histogram and or the vertical bending parameter File Edit View Reports Tools Help PW PIS RACO OFAR IS 2h Sh dN S We tH Add Files to Project Adjust Contrast Ow Wx 2 Image Pool Contrast Modified een oats DA 3524 22459 Unit Intensity Region Whole Image v Colors Gray v C Invert Workspace _ Adjust Contrast Gels 12 Spots0 Annotations 0 Apply 7 To view saturated and background regions in the images change the palette in the Color drop down list to Gray Saturation Note You can redefine the preview regions to look at other areas in the images 6 Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 8 To apply the contrast settings to all selected images reset the Color drop down list to Gray and click Apply 9 Close the Adjust Contrast window Modifications such as rotation flio and crop are simultaneously carried out on all the images in a single DIGE gel 1 4 View the Workspace 1 To open the Workspace if not already visible click the Workspace tab on the left side of the interface 2 To pinthe Workspace click the Auto Hide button in the top right corner of the window
18. ols will only become visible once the landmark has been validated in the reference In the example the landmark had to be validated in the image B_T2_Gell before any 14 Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 landmark symbols would appear in the images B_T2_Gel2 and B_12 Gel It is sufficient to place just one or two landmarks in gels with good reproducibility 1 9 Match gels 1 Choose Edit gt Matches gt Match Gels or click Match Gels in the toolbar if present 2 Use the Ctrl or Shift keys to choose the match sets to be matched IN principle all of them can be selected Click OK File Edit View Select Reports Tools Help OAR SO RB COiOG ACR aseds pon a ye eter SO When the process is completed the software gives the number of matches created and displays the match vectors in blue Vectors link the spot in a gel with the corresponding spot in the reference image imagine that the reference lies below This reference image should not be mistaken for the match reference The vector pattern is proof of consistency If there is a mismatch the vector has a different length and or orientation Melanie 7 0 Quick Start Manual Edition AA 1 Melanie Quick Start 1 10 Edit matches When a gel is moved the vectors become longer Select Move in the toolbar and double click in the gel to recenter all the images including the reference to the same position and therefore min
19. se the buttons in the top right corners of the window When docking a window blue arrows indicate where the window may be docked By moving the cursor over the arrows a shaded blue box shows where the window will reside once the leff mouse button Is released To preview the spot detection results click Region in the toolbar to define a region in one or more selected gels in areas with representative spots To display the Cursor Information window click Cursor Info in the toolbar Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 3 Choose Edit gt Spots gt Detect or click Detect in the toolbar if present 4 Inthe Detect Spots window adjust the Smooth parameter to detect all real soots and correctly split any overlapping ones 5 Move the cursor over a few spots that you consider to be noise or artifacts and look at their Saliency values in the Cursor Information window In the Detect Spots window enter a Saliency value that is just above that of the spots to be filtered out 6 Sometimes very small but intense artifacts like dust particles cannot be eliminated with the Saliency parameter without removing real spots To get rid of such artifact spots set an appropriate Min Area value 7 When the detection preview Is satisfactory click OK to detect all spots in the selected gels File Edit View Select Reports Tools Help iW PlEIk SO RM CO 0OGP R Cursor Information Or x RAB Properties Values Fil
20. the Class Analysis Table 3 Choose Reports gt Analyse Classes gt Table 4 To pin the Class Analysis Table window open click the Auto Hide button in the top right corner The title of the table indicates that the Center and Dispersion values for each class e g AT AT2 BT and BI2 correspond to the Mean and M S D respectively Class Analysis Table Mean 100 and M S D Say ed Y A H center F BT2 eeesveresevererererererenereve aye ae j DE z ae es ore Re to ee i ies Ere 3 2 0 00411455 0 00411 0 00133375 4 3 0 285252 0 254237 0 140067 0 233544 0 285252 5 4 0 0548193 0 0205532 0 0548193 0 040103 6 5 0 0312753 0 0153396 0 0216184 0 0200948 0 0312753 7 6 0 101042 0 0438242 0 101042 0 0523737 Click the Statistics drop down list in the table toolbar to change the statistical values displayed Note The sliders in the Classes Statistics window allow you to remove a percentage of outliers for the calculation of the Central 20 Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 tendency and Dispersion By default no outliers are excluded You can also set the two classes to be used for the calculation of the Student t Mann Whitney U and Kolmogorov Smirnov D statistics Classes Statistics cG HX Choose the statistics The sliders restrict the statistics to the central values Central tendency Mean Midrange Dispersion Mean squared deviation gt 100
21. to view the gel name Classes are separated by gray vertical lines The blue horizontal lines in the histograms represent the mean values for each class The red lines delimit the class intervals defined by Central value Dispersion Central value Dispersion These notions relate to the Overlapping Measures that are calculated by Melanie in the Class Analysis Table Gap Maximum difference between the range of the current class and the range of one of the other classes Negative values indicate overlapping intervals whereas positive values are non overlapping intervals Ratio Maximum ratio between the lower limit of one of the other classes and the upper limit of the current class Absolute values less than 1 indicate overlap whereas absolute values greater than 1 show that there is no overlap If one class interval is completely overlapped by another one the Ratio is 0 Negative values indicate that the spots in the current class are under expressed compared to those in the other class Note The default Ratio is not the widely used ratio between the mean values in two classes To calculate this classical ratio you must set the Dispersion slider in the Classes Statistics window see above to 0 Melanie 7 0 Quick Start Manual Edition AA Melanie Quick Start 1 e Normalized Maximum percentage of the current class range not overlapping with the range of one of the other classes A value less than 1 indicates overlap For exa
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