GPR Analyzer version 1.23 – User`s Manual
Contents
1. 8 sl ie deoa cC 8 The math behind S N ratios total intensity and normalized MEAN cccccssscccessseceeessececessaececeessececseseeeseaaes 9 Calibration ata EE n 9 Inferring cell concentratiOns 5 icri inerte tera en EFE PR e kou Fes ERR EAR AR EXU EE REF U Ya FRE ANN FERE EE FUE EAR AREE EKR EN VES REF REA Pad 10 The hybridization specific detection limit essseeessessese eene enne enne nene ener en nennen enne 11 BITTE 11 Frequently asked questioris FAQS ornetur ran er Ee XE REA RED XR RR TR EAR RR PR aes Re ep ade dba 12 MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 1 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE GETTING STARTED INSTALLATION AND SYSTEM REQUIREMENTS GPR Analyzer should run on any system Windows Linux Mac with a recent version of a JAVA runtime environment JRE It was tested on Windows 7 64 bit Java 1 6 0 21 and Mac OS X Snow Leopard Java 1 6 0 29 Windows users can download a JRE free of charge from Oracle at this address http www java com en download index jsp GPR Analyzer does not require any installation Simply unpack the zip archive into a folder of your choice and double click the GPRTransformer1 23 jar file If you downloaded a bundle specifically for Windows or MacOS you can also double click on the cor2. differences in the standards or also by differences in the cellular RNA content of your species Cell numbers are only calculated if calibration data is available for the current species of interest and the selected normalization probe Hierarchy check information Hierarchy This column displays the results of the Hierarchy check For all probes that are above the selected signal to noise cutoff the program will check if any higher level probes are present on the microarray and if so if these probes are above your cutoff as well If all higher level probes are also above your threshold the result will be PASS and the probes that were tested will be listed in parentheses If e g a species specific probe is above your threshold but the corresponding genus probe is not the result of the Hierarchy check will be FAIL and lists of higher level probes that either passed or failed will be given in parentheses Information about the hierarchical structure of the probes is saved in the hierarchy file see below If no higher level probe is present on the array this field will be left blank If the hierarchy file indicates a higher level probe that was not found on the array the result will be Missing and the probe s not found will be given in parentheses Color highlighting To make it easier for you to get an overview over your data GPR Analyzer uses a green background to highlight probes that have a signal to noise ratio
3. DphyFS02 25 dT gt DinoB 25 dT DphyGS02 25 dT DphyGS03 25 dT DphyexacutaFS01 25 dT gt DphyFS02 25 dT gt DinoB 25 dT DphyGD01 25 dT DphyGS03 25 dT gt DphyexacutaFS01 25 dT gt DphyFS02 25 dT DinoB 25 dT Dnor S01 25 dT gt DphyGS03 25 dT DphyexacutaFS01 25 dT DphyFS02 25 dT gt DinoB 25 dT DacutaD02 25 dT gt DphyFS02 25 dT gt DinoB 25 dT DacutaS01 25 dT gt DacutaD02 25 dT gt DphyFS02 25 dT DinoB 25 dT Return to main program Figure 5 Hierarchy viewer integrated into GPR Analyzer Each probe is followed by a list of probes that should also be active if the first probe is If this is not the case the signal for the first probe may be a false positive and the hierarchy check will return FAIL as a result As described above GPR Analyzer uses hierarchical probes to perform internal validation and to identify false positive probes This principle of validation has previously described and been implemented by Metfies et al 2008 Mol Ecol Res 8 99 102 GPR Analyzer supports the same XML format for hierarchy files as Phylochipanalyzer as well as a simpler tab separated text format The default hierarchy file for GPR Analyzer is stored in the hierarchy hir file It can be viewed using the Tools Hierarchy menu where there is also the possibility of loading alternative hierarchy files in either xml or hir format Figure 5 If you would
4. OF TOXIC ALGAE FOR ADVANCED USERS HIERARCHY DATA KE Hierarchy Viewer hierarchy hir Import hierarchy Export as hir file 3XSSC E POSITIVE 25 dT Poly T CY5 EEGATIVE1 dT INEGATIVE3 25 dT ukS 328 25 dT ukS 1209 25 dT EukS 328 25 dT DunGS05 25 dT dT EukS 1209 25 dT gt EukS 328 25 dT DunGS02_25 gt EukS 1209 25 dT gt EukS 328 25 dT est15 EukS 1209 25 dT gt EukS 328 25 dT DunGS02 25 dT dT EukS 1209 25 dT gt EukS 328 25 dT est12 gt EukS 328 25 dT EGATIVE2 25 dT DinoB 25 dT DinoE12 25 dT DinoB 25 dT DphyFS02 25 dT gt DinoB 25 dT DphyexacutaFS01 25 dT gt DphyFS02 25 dT DinoB 25 dT DphyGS03 25 dT DphyexacutaFS01 25 dT DphyFS02 25 dT DinoB 25 dT DacumiD02 25 dT DphyGS03 25 dT gt DphyexacutaFS01 25 dT DphyFS02 25 dT gt DinoB 25 dT est18 DacumiD02 25 dT gt DphyGS03 25 dT DphyexacutaFS01 25 dT DphyFS02 25 dT DinoB 25 dT DacumiS01 25 dT DacumiD02 25 dT DphyGS03 25 dT DphyexacutaFS01 25 dT DphyFS02 25 dT DinoB 25 dT DacumiD02 25 DacumiD02 25 dT gt DphyGS03 25 dT gt DphyexacutaFS01 25 dT DphyFS02 25 dT DinoB 25 dT DphyGS04 25 dT DphyGS03 25 dT DphyexacutaFS01 25 dT DphyFS02 25 dT gt DinoB 25 dT DphyGS01 25 dT gt DphyGS03 25 dT gt DphyexacutaFS01 25 dT gt DphyFS02 25 dT gt DinoB 25 dT DphyGD02 25 dT DphyGS03 25 dT gt DphyexacutaFS01 25 dT
5. a filter from a plain text file listing the name of each probe you want to display in a separate line each This is done via the Tools gt Filter gt Load filter menu The second possibility is to edit a filter manually This can be done via the Tools gt Filter gt Edit filter menu BE Filter Editor x 3XSSC axssc a POSITIVE 25 dT ATNA D01 25 dT m a ATNA D02 25 dT ATTA D01 25 dT EGATIVE3 25 dT zd EukS 228 25 dT AlexGD01 25 dT ukS 1209 25 dT AminuS01 25 dT L unGS05 25 dT dT lAostD01 25 dT unGS02 25 AostS02 25 dT est15 AtamaS01 25 dT unGS02 25 dT dT AzaGD01 25 dT est12 AzaGD03_25_dT p ii AzaGS01 25 dT inoE12 25 dT AzaGS02 25 dT phyFS02 25 dT Clade 01new25 dt phyexacutaFS01 25 dT Clade010ld 25 dT phyGS03 25 dT CompPdel3 25 dT acumiD02 25 dT CpolyS01 25 dT est18 CtoxS05 25 dT acumiS01 25 dT CtoxiS05 epit ay CtoxiS07 25 dT dieit 25 dT CtoxiS09 25 dT phyGD02 25 dT DacumiD02 25 phyGS02 25 dT DacumiD02 25 dT phyGD041 25 dT DacumiS01 25 dT norS01 25 dT DacutaD02 25 dT acutaD02 25 dT DacutaS01 25 dT acutaS01 25 dT DfarD01 25 dT rotuS01 25 dT DinoB 25 dT L Kare0308A25 dT bi E12 25 aT L Kare0308A25_dT DinoE12 29 1 i jd nor S04 25 dT s Apply changes cancel M Figure 4 Filter editor It can be accessed via the Tools gt Filter gt Edit filter menu and provides a text field left which can be used to enter all probes of interest in a specified
6. like to convert a Phylochip xml file to a hir file first load the XML file using the Import hierarchy button Tools gt Hierarchy and then the Export as hir file button XML based hierarchy files can be customized using an XML enabled text editor or Phylochip Analyzer tab separatated hir files can be edited e g using a text editor or a spreadsheet application such as Excel Each line contains the name of a probe on the chip as well as MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 8 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE o oS Senes CE E DU list of all higher level parent probes All probe names are separated by tabs Empty lines or comments starting with are ignored by GPR analyzer The advantage of the hir as opposed to the xml file is flexibility Let s assume you have two probes p1 and p2 on the same hierarchical level targeting the same organisms Using a hir file you can then define p1 as parent to p2 and at the same time p2 as a parent for p1 This way p1 and p2 will only pass the hierarchy check if both are above the cut off Using the Phylochip xml format you can only define either p1 as parent for p2 or p2 as a parent for p1 but not both This way one of the two probes may pass the hierarchy check even if the other is not above the cut off THE MATH BEHIND S N RATIOS TOTAL INTENSITY AND NORMAL
7. of the present species in a sample It is assumed that all calibration curves cross the x axis at x20 i e that no signal is obtained if no RNA is hybridized INFERRING CELL CONCENTRATIONS The most important step for inferring cell numbers is to divide the normalized signal obtained for a probe of interest using a given normalization probe by the normalization factor for the same probe of interest and same normalization factor in the calibration file Since this factor corresponds to a slope of a calibration curve plotting normalized signals against cell numbers this simple division will yield a first estimate of the cell number A number of different components see Formulas section in the calibration file can be added to this formula to take into account different experimental setups and different probes used for normalization Volume filtered The first factor is the volume filtered for your extraction This will allow the calculation of cell concentrations rather than absolute cell numbers by dividing the inferred cell number by the volume Liters in the Formulas section Dunaliella cells added The default way of normalizing in the MIDTAL Project is by adding a defined number Dunaliella cells to the field samples and by using the signal obtained from a Dunaliella specific probe DunGSO2 25 dT dT Since everything that is done with your sample is also done with the added Dunaliella cells no additional factors need to be consider
8. the species of interest are present in the sample or not especially considering that the detection limit may vary strongly depending on the quality of the hybridization and the quantity of material hybridized To help users evaluate negative results hybridization specific detection limits are estimated These calculations are essentially the same as those to calculate cell numbers except that they are based on a hypothetical total signal which is the hypothetical signal intensity that would have yielded a signal to noise ratio corresponding to the cutoff This hypothetical total signal is calculated based on the local background of the relevant probes but assuming the spot diameter set for the probe used for normalization The diameter of the normalization probe is used to avoid problems that may occur the scanner software is set to detect spot diameters automatically but fails to do so correctly when the signal for the probe of interest is low The inferred detection limits are shown in GPR Analyzer after a sign for probes with available calibration data and a signal to noise ratio below the detection limit and above 1 DISCLAIMER Please note that the calculated cell numbers and detection limits are only very rough approximations of what may be found in a field sample They will depend on the cellular RNA content in your sample and may vary significantly depending on how many factor are considered in the calculations Most importantly cell nu
9. GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE GPR Analyzer version 1 23 User s Manual GPR Analyzer is a tool to quickly analyze multi species microarrays especially designed for use with the MIDTAL Microarray Detection of Toxic ALgae chip It will read Genepix GPR files produced by scanner software and perform probe averaging and normalization infer cell concentrations and perform internal validation of the results taking advantage of hierarchical probes CONTENTS Getting Started ES 2 Installation and system requirements cccccceesseececeeeeeecseeeeceeqeeeeecseeaececeeeeceeueeececenaecesseeeceeueeeceeeeeseessneeeeeeas 2 LO AGING a epr TOs ETT DDR m 2 Entering metairniftOTatlO coiere terrre patre ina roodo see oa dep eva ees npe TEE EE EEP ree EVE ed ars pea TRADE aede EER 2 Displ ying VOUP Gata ER E 3 Changing your normalization probe eseesssssssseeeeeeeeeee eene enne nennen enne nn niens nens sten nensis enses tense nennen 6 Working WAC TITS HS 5 iioc euenire eene s Dev va ue ee ar depend NER bia Pug A Yu ae n nao Fea e no da gu SEE ERN RES 6 Exporting results 2 cuisine pet ka aae nonae FR Re ene a ERE HEREIN Exe Fea ae o Reano Ce REDE ieia ie AREE eM Re Reano xa vat 7 CHECKING for updates ete dete e iaa e aaa eies Bea e eun Era nega ANE EUER NE UAR e ERR PUR RV aaae 7 For AGVANCEM ETC
10. IZED MEAN These three parameters are the basis of all analyses Each of these values is calculated from a number of values extracted for each spot from different columns of the GPR file They are B635 Mean F635 Mean and Dia and correspond to the mean fluorescence at 635 nm for the spot the mean fluorescence of the local background and the diameter of the spot respectively The Name column is used to name probes and group identical probes for averaging The signal to noise ratio is calculated as F635 Mean B635 Mean Mean and standard deviation are calculated for the ratios of all active probes with identical names The total signal intensity is calculated as F635 Mean B635 Mean Dia Dia 4 3 14159 the latter part corresponding to the area of the spot Mean and standard deviation are calculated for all total signal intensities of active probes with identical names Total intensities O are automatically set to O Normalized signals are calculated by dividing the total signal intensity calculated for each spot by the average total signal intensity of the probe designated as normalization probe Mean and standard deviation are calculated for all normalized signals of active probes with identical names CALIBRATION DATA Default calibration data are stored in the caldata dat file and used to infer cell numbers based on the normalized signals but you can temporarily load other calibration files us
11. If you are calibrating your array with a standard you have added after taking an aliquot of your sample for the hybridization two additional pieces of information need to be considered how much RNA was extracted from your sample and how much of that was spiked with your standard Both pieces of information can be entered 7 in the Tools Edit sample information menu If RnaRatio is selected in the Formulas section your inferred cell number will be multiplied by your total RNA extracted and divided by the amount of RNA used for the hybridization Degree of labeling If your standard positive control is already labeled and added after the labeling step you can consider differences in the labeling efficiency degree of labeling DOL for your sample and for the samples used in the standard curve The DOL is calculated as 0 34 ng pmol Cy5 Concentration in the labeled extract in pmol ul RNA concentration in the labeled extract in ng l 10096 This corresponds to the proportion of labeled bases in your sample If DOL is activated your inferred cell number will be multiplied with DOL in your calibration curves and divided by the DOL in your sample In the calibration file that comes with the program all DOLs were normalized to 296 THE HYBRIDIZATION SPECIFIC DETECTION LIMIT In some cases probes may have signal to noise ratios only slightly below your detection limit In such cases it is difficult to tell if algae of
12. above your cutoff and that have not failed the hierarchy check either no higher level probes were available or all higher level probes were also above the threshold Probes with a signal to noise ratio above the threshold that have failed the hierarchy check are marked in yellow Probes below the cutoff have a white background MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 5 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Sorting the table You have the possibility of sorting your data according to any column just by clicking on the column name Click on the same name again to reverse the order Please note that cell numbers are sorted alphabetically because they contain a mixture of numbers and non numerical characters lt Another way of sorting your data is by using filters see below CHANGING YOUR NORMALIZATION PROBE The Tools gt Settings menu allows you to choose any probe from normalization The default probe is DunGSO2_25_dT_dT Please note that the Probes list on the right hand side of the Settings dialog will only be filled with probe names if you have already loaded a gpr file Figure 3 For more details please refer to the calibration data section below WORKING WITH FILTERS Filters can be used to display only a subset of probes of interest in a specified order There are two ways loading a filter into the program One option is to load
13. e 444 R IBEEETPTCEEER D last column contains a label for the values calculated with the formula e g Cells Cells L or ng target RNA The Factors section contains information about your calibration curves The first column indicates the name of the factor described the second column contains the corresponding value The factors considered are DOL Degree of labeling for your calibration curve DunCell the number of Dunaliella cells added for your calibration curve and ngPC ng of positive control added for your calibration curve Not all of the factors will be used for all calculations depending on the formulas defined in the Formulas section Please note that only one value per factor can be entered for all calibration curves If you are preparing your own calibration file and if some calibration curves were carried out differently from others these will have to be normalized to standard conditions first The Data section contains the actual calibration information for an individual probe The first column indicates the name of the probe for which the calibration data is valid the second the species used for this calibration curve The following columns indicate the calibration factors for each of the possible normalization probes in the same order as defined in the Formulas section The calibration factor is the slope of a calibration curve plotting the normalized signal against the number of cells
14. eck 237 151 157 547108 v 194 202 0 96 r 273 212 129 wi 352 a75 1201 a x 2t M ues r Information about individual spots tosiilillis FORTHE D ON OF TOXIC A for the currently selected probe Figure 2 Overview of the interface The upper table displays probe averages while the lower table details about the spots i e features associated to the currently selected probe This the top table may be customized using the Tools gt Settings menu MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 3 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE The spot table the lower one allows you to examine mean fluorescence Fmean mean background Bmean as well as the signal noise ratio and the total signal intensity for each probe You can also choose to activate or deactivate an individual spot by clicking on the corresponding check box Only active spots will be used for the calculation of the data shown in the probes table Spots with an Fmean and a Bmean of 0 are deactivated by default Please note that it is advisable to identify and remove low quality spots already during image analysis as more information about the context is available If you find strong differences between spots form different blocks please re check your image The columns displayed in the probe table the upper one can be customized according to your needs via the Tools gt Sett
15. ed with this method However it is necessary that the calibration curves and your samples were spiked with the same number of Dunaliella cells added If this was not the case this can be corrected for and this is why it is necessary to add the number of Dunaliella cells added both to your sample information and to the calibration data DunCell in the Formulas and Factors sections If DunCell is activated in the Formulas section your inferred cell number will be divided by the number of Dunaliella cells added in the calibration curves and multiplied by the number of Dunaliella cells added to your sample Quantity of PC used MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 10 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE no os Sears CLUN E If DNA or RNA based standards are used for calibration PC positive control the same quantity of standard needs to be added to your sample and to the samples used to generate the calibration curve If this was not the case this can be corrected for via the ngPC option If ngPC is activated in the Formulas section your inferred cell number will be divided by the quantity of standard added in you calibration curves and multiplied by the quantity of standard added to the sample Mathematically this option is identical to the Dunaliella cells option but the extraction efficiency is not considered RNA ratio
16. equired depend on the probe used for normalization and the corresponding formula By default the number of Dunaliella cells added prior to the extraction and the volume filtered will be required if you are using the DunGSO2 25 dT dT probe for normalization The total quantity of RNA extracted from your sample as well as how much was used for your hybridization will be required for standards added to the hybridization buffer The degree of labeling for your sample is required only if the standard is already labeled and added after the labeling step Please note that should be used as decimal separator Data that was entered incorrectly will be highlighted in red when you press ok Should you wish to modify the sample meta information at a later point in time please select Tools Edit sample data to return to the dialog see Figure 1 MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 2 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Please enter Sample information olume filtered L otal RNA extracted ng otal RNA in hybe ng Dunaliella cells added 500000 Quantity of PC used ng 100 Figure 1 Dialog for entering sample metadata It is egree if labeling 2 automatically displayed when loading a gpr file or can be accessed via the Tools gt Edit sample data menu DISPLAYING YOUR DATA The main display in GPR Analyzer consists of t
17. fferences in the background noise Standard deviation of total signal Total SD The standard deviation of the mean total signal calculated for the active replicate spots Mean normalized signal Norm This is the total signal of the current probe divided by the signal of the selected normalization probe The normalized signal should be independent of your scanner settings the quality of your hybridization and depending on when your standard was added also of the labeling and extraction efficiency in the case of Dunaliella as a standard Standard deviation of normalized signal Norm SD The standard deviation of the mean normalized signal calculated for the active replicate spots Inferred cell number Cells L This number is an estimate of the cell concentration for a specific species in your original sample in cells per liter based on the sample information you have entered and the available calibration data It is calculated only for probes with a signal noise ratio greater than your cut off see Tools gt Settings If your signal to noise ratio is between 1 and your cut off the program will calculate the number of cells that theoretically would have been necessary to yield a signal corresponding to your cutoff see below This number is displayed following the lt sign and can be used as a rough indication of your detection limit Please also consider that the inferred cell numbers may be biased by unspecific signals
18. ies Your calibration file see below may contain information relating probe names to species If this information is available for a probe it will be displayed in this column Number of spots Spots This column displays the number of replicate spots for a probe currently considered for the calculation before the and the total number spots available for this probe after the Mean signal noise S N This is the ratio of the mean signal of a probe and the local background signal The signal to noise ratio is an important measure to determine if a probe is highlighted or not A corresponding cut off can also be set in the Tools Settings menu and will affect the calculation of cell numbers the hierarchy MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 4 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE o os Senes CS E DU check and color highlighting see below As a rule of thumb a signal to noise ratio gt 2 is used as an indication that labeled RNA has bound to your probe Standard deviation of signal noise S N SD The standard deviation of the mean signal to noise ratio calculated for the active replicate spots Mean total signal Total The total signal is used to quantify how much labeled RNA has bound to a probe and thus was present in your sample It is used to calculate the normalized signals and to infer cell numbers as it is not easily affected by di
19. ing the File gt Load alternative calibration menu GPR Analyzer calibration files are commented tab separated text file which can be edited in common spreadsheet applications please note that the decimal separator must be Empty lines and comments starting with are ignored by the program The calibration file consists of four sections Version ap Formulas Factors and Data each of them is started by and followed by the name of the section The Version section consists of a single line containing Version followed by the version number of the current calibration file If you have a costume calibration file and you wish to disable automatic updates please set the version line to IVersionznoupdate The Formulas section contains one line for each normalization probe with available calibration data followed by five columns with TRUE or FALSE values depending on which blocks of the formula to infer cell concentrations see Inferring cell concentrations should be activated The order of columns is indicated in the file by a comment and is Degree of labeling Dunaniella cells spiked Ratio of total extracted RNA and RNA used for the Hybridization Liters filtered and ng of positive control added to the hybridization The MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 9 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE eL I
20. ings menu where you can select the columns to display in the Output section The information displayed in each column is described below S Setting dialog Normalization Probes select probe or enter name 3XSSC DunGS02 25 dT dT ATNA D01 25 dT ATNA D02 25 dT Detection limit ATTA D01 25 dT Select signal noise cutoff default 2 AAlexGD01 25 dT 2 0 J AminuS01 25 dT AostD01 25 dT Output AostS02 25 dT Species used for calibration AtamaS01 25 dT Number of spots AzaGD01 25 dT AzaGD03 25 dT AzaGS01 25 dT Standard deviation of signal noise AzaGS02 25 dT v Mean signal noise ratio Mean total signal Clade 01new25 dt Clade010ld 25 dT CompPdel3 25 dT Mean normalized signal CpolyS01 25 dT C Standard deviation of total signal C Standard deviation of normalized signal CtoxS05 25 dT CtoxiS05 y CtoxiS07 25 dT Hierachy check information CtoxiS09 25 dT decimal separator DacumiD02 25 DacumiD02 25 dT DacumiS01 25 dT DacutaD02 25 dT DacutaS01 25 dT Inferred cell number Figure 3 Tools gt Settings dialog This dialog is used to set the normalization probe signal to noise ratio and output options The list of probes on the right hand side is only available if a gpr file was loaded All settings are automatically saved if you press Apply changes and will remain active even if you restart the program Species used for calibration Spec
21. mbers will be under estimated if probes are saturated MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 11 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE FREQUENTLY ASKED QUESTIONS FAQS If you are experiencing problems with GPR Analyzer please write an email to simon dittami bio uio no will try to answer your question or in case of a bug report to fix the problem Why is the cell number column empty The reason for this is usually that no calibration data is available for the probe used for normalization Please ensure that the caldata dat file is present in the GPR Analyzer directory and select a probe with calibration information to normalize your data Please also enter all the necessary metadata for your hybridization Calibration data is currently not available for all species probes MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 12 of 12
22. ols gt Filter gt Save filter command from the main menu EXPORTING RESULTS The results of your current analysis the probes table can be exported either by using the File gt Export TXT command or using the Copy button in the top right corner of the program Using either option a tap separated text will be generated and either saved as a file or copied to your system s clipboard This tab separated text can then be opened by or pasted to other application such as Excel or OpenOffice Calc for further analysis The exported data will comprise all columns currently visualized in the probe table Any sorting or selection of probes using filters will be considered for the export but sorting of the probe table by clicking on column names has no effect on the order in which probes are exported Please note that the current version of GPR Analyzer supports only an export in the plain text format Thus color highlighting can presently not be included In addition for use with spreadsheet programs such as Excel un please ensure that your system s decimal separator is set to or that you change the decimal separator option in GPR Analyzer under Tools Settings to match that of your system This option affects only the way numbers are exported not the way they are displayed within the program which is determined by the version of JAVA running on your machine CHECKING FOR UPDATES You can use the About Check for u
23. order Only one probe can be entered per line Double clicking on a probe in the probe list on the right will insert the probe at the current cursor position MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 6 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE no os eeare S RAE DU The filter editor Figure 4 consists of a large text field which can be used to enter the list of probe names either manually or by copy pasting it from another application A complete list of probes found in your current gpr file is available on the right hand side of the filter editor if a gpr file is loaded You can insert a probe name at the current cursor position in the text field simply by double clicking on the probe in the list Please make sure that only one probe is entered per line Multiple probes per line or probes not found in your gpr file will be omitted Another option is to automatically generate a filter based on the probes and the order of the probes found in your hierarchy file This is done by pressing the Import from hierarchy button in the filter editor The filter you have loaded or created will automatically be activated unless you choose cancel in the editor It can later be deactivated and reactivated using the Tools gt Filter gt Deactivate filter and the Tools gt Filter gt Activate filter menus You can also save your current filter for later use using the To
24. pdates option to see if a newer version of GPR Analyzer or of the calibration data is available If new calibration data is available online you can choose to update your caldata dat file without restarting the program Your old calibration file will be backed up as caldata bak or caldata bak n where n is a number increasing with each backup found If the update fails e g because the connection to the server breaks down you can either manually restore your previous calibration file by renaming the latest backup file to caldata dat or you can retry running the update again later If you update your calibration file while analyzing a GPR file the metadata you have entered for your sample will be overwritten by the default metadata defined in the calibration file In order to update the main program you will need to visit the indicated web site download and unpack the contents of the zip file into your GPR Analyzer directory manually GPR Analyzer comes bundled with default settings hierarchy and calibration files If you wish to keep your current files when updating choose no when you are prompted by your operating system to overwrite the settings ini caldata dat and hierarchy hir files Please note that checking for updates and the automated update requires an active network connection MICROARRAYS FOR THE DETECTION OF TOXIC ALGAE Page 7 of 12 GPR Analyzer v1 23 Feb 27th 2012 MANUAL MICROARRAYS FOR THE DETECTION
25. responding exe file or the app bundle instead Please note that file extensions the part after the last may be hidden depending on your system settings The program should appear on your screen For the program to work properly please ensure that you have write access to the directory you chose and do not remove any of the files found here caldata dat hierarchy xml and settings ini LOADING A GPR FILE gpr files are generated by your scanner software To load one of these files choose File gt Import GPR If you wish to load a different file choose File Import GPR again and select a different file The current data will be discarded and the new data loaded If you do not have a GPR file available you can start with a file from sample data folder in the GPR tansformer directory If you have technical replicates you wish to analyze at the same time you can load additional replicates using the File Import replicate GPR command This option will add another gpr file to your current analysis ENTERING METAINFROMATION When you load a GPR file you will be asked to enter additional information about your sample These data are necessary in order to calculate estimates for the number of cells present in your sample The actual calculations are detailed below If essential fields are left blank no cell numbers will be calculated and the corresponding column will be blank The fields r
26. wo tables the top table displaying summaries for each probe referred to as Probe table and the bottom table containing detailed information about the replicate spots features for the currently selected probe referred to as Spot table Figure 2 Current gpr file Main menu Click here to sort contents by values in a column v sec 3 EM uim vid Copy table to clipboard File Tools About Copy Probe der SN Nom Cells I Hoover over a cell to display the z complete contents IPcaciD01 25 dT Pseudo nitzschia calliantha 1 08 0 0051 267417 Pman2D02 25 dT Pseudo nitzschia calliantha 1 66 0 059 lt 3212171 IPman2D05 25 dT Pseudo nizschiacalllantha 154 0 03 1043956 FAIL failed PsnGS01_25_dT passed PcaserausD03_25_dT PSN no pungens 25 dT PSN FragS01 HeteroS01 25 dT 2 35 ASS passed PsnGS02 25 dT PschGS0 6 24 ASS passed HeteroS01 25 iiin A probe above the cutoff that ae passed PenG502_25 dr UeehGSn passed the hierarchy check d755 PASS passed PrymS02 25 dT 98 89 10 25 11 1149 96116 ASS sed an IPparvD01 25 dT Prymnesium parvum 159 0 04 341758 A probe with a negative signal LSKbKmo548A25 dT Karenia mikimotoi 102 00065 9701 Spots Probe Fmean Bmean SN Total Active DfarD01 25 dT 242 433 1 82 1693427 r A probe above the cutoff that j 220 128 1 72 1040495 v M 256 135 19 1606059 a failed the hierarchy ch
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