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1. error equation page 228 Additive error component in Red channel 160 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Description float Ratio_AddErrorGreen Additive error component in Green channel float Ratio_MultErrorRed Multiplicative error component in Red channel float Ratio_MultErrorGreen Multiplicative error component in Green channel integer Ratio _UseSurrogates Flag indicating the use of surrogates Use of surrogates turned on Use of surrogates turned off text FeatureExtractor Software component ID GUID of Feature Extractor text FeatureExtractor_Version Version of Feature Extractor text FeatureExtractor_ArrayName Microarray filename text FeatureExtractor_ScanFileName Name of the Scan File used for Feature Extraction text FeatureExtractor_ScanFileGUID GUID of the Scan File text FeatureExtractor_Barcode Barcode of the microarray text FeatureExtractor_DesignFileName Design or grid file used for FE text FeatureExtractor_PrintingFileName Print file if available used for FE Agilent G2567AA Feature Extraction Software v 7 5 User Manual 161 6 Settings and Results Statistical results STATS This middle section of the text file describes the results from the statistical calculations Table 18 Stats results contained in the text output file STA2. is the g r MeanSignal of the corresponding deletion control or zero if no deletion control exists If the corresponding deletion control exists then the perfect match error is the propagated standard error as calculated on the raw perfect match signal if no such deletion control exists then its value is the background subtracted error This is the propagated standard error as calculated on the raw deletion control signal or zero if no deletion control exists The p value for the t test that tests if a perfect match probe is equal to its deletion control in the g r channel g r PerfMatchSignal fails positive and significance t test 0 01 versus its g r DelCtrlSignal and deletion control passes g r lsWellAboveBG Feature passes g r lsWellAboveBG and additionally the g r PerfMatchSignal is positive and significant t test p value lt 0 01 versus its g r DelCtrlSignal 172 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description float boolean float float float float gPMDLratio IsNormalization gDyeNormSignal gDyeNormError DyeNormCorrelation ErrorModel xDev rPMDLratio rDyeNormSignal rDyeNormError 1 Feature used 0 Feature not used 0 Propagated model chosen by you or by software 1 Uni
3. subtract from the MeanSignal variable also used in t test To view the values used to calculate this variable using different background signals and settings of spatial detrend and global background adjust see Table 29 on page 214 Standard deviation of background used in g r channel variable also used in t test and surrogate algorithms To view the values used to calculate this variable using different background signals and settings of spatial detrend and global background adjust see Table 29 on page 214 If deletion controls exist then this is the corresponding feature number Agilent G2567AA Feature Extraction Software v 7 5 User Manual 171 6 Settings and Results Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Description text float float float float float boolean boolean DelCtriProbeName gPerfMatchSignal gDelCtrlSignal gPerfMatchError gDelCtrlError gPValPerfMatchEg DelCtrl glsLowSpecificity glsGoodPM rPerfMatchSignal rDelCtrlSignal rPerfMatchError rDelCtrlError rPValPerfMatchEq DelCtrl rlsLowS pecificity rlsGoodPM If deletion controls exist then this is the corresponding probe name If the corresponding deletion control exists then the perfect match signal g r MeanSignal if no such deletion control exists then its value is the background subtracted signal This
4. 59 6 Settings and Results Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Options Description integer float float integer float text text integer integer integer float float float DyeNorm_CorrMethod DyeNorm_RankTolerance DyeNorm_LOWESSSmoothFactor DyeNorm_LOWESSNumSteps DyeNorm_LOWESSDelta Ratio Ratio_Version Ratio_ErrorModel Ratio_AutoEstimateAddErrorGreen 1 Ratio_AutoEstimateAddErrorRed 1 Ratio_MultNCAutoEstimate Ratio_MultRMSAutoEstimate Ratio_AddErrorRed Methods for computation of dye normalization factor to remove dye bias Linear Linear amp LOWESS locally weighted linear regression preceded by linear scaling in each dye channel LOWESS locally weighted linear regression Correlation of feature in red and green channels Smoothing parameter for LOWESS curve fitting Number of iterations in LOWESS Minimum spacing between points used in LOWESS GUID of Ratio algorithm Version of Ratio algorithm Selected Error Model Hybrid Model Propagated Error Universal Error Model Auto estimation turned on Auto estimation turned off Auto estimation turned on Auto estimation turned off Multiplier for the first term standard deviation of the inlier negative control in the additive error equation page 228 Multiplier for the second term g r SpatialDetrendRMSFit in the additive
5. 6 Settings and Results Results Output Text file results See View and interpret text results on page 37 for instructions that show you how to view the text file results Results are reported to 9 decimal places in exponential notation for all result files Also all dimensions and distances are now in radii and pixels not diameters or microns This means that the reported values for width and height measurements must be multiplied by 2 to obtain the width and height for the spots Feature Extraction produces a tab delimited text file that contains three tables of input parameters and output results These tables are FEPARAMS STATS and FEATURES The FEPARAMS table contains input parameters and options used to run Feature Extraction The STATS table gives results derived from statistical calculations that apply to all features on the microarray The last table FEATURES displays results for each feature in over 90 output columns such as gene name log ratio processed signal mean signal or dye normalized signal Parameters options FEPARAMS The top most section of the result file contains the parameters and option choices that you used to run Feature Extraction Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Options Description text FeatureExtractor_UserName Windows Log In Name of the User who ran Feature Extraction text FeatureExtractor_Compute
6. TS table Type Stats Green Channel Stats Red Channel Description float gDarkOffsetAverage rDarkOffsetAverage Dark offset data per image per channel as measured by scanner float gDarkOffsetMedian rDarkOffsetMedian float gDarkOffsetStdDev rDarkOffsetStdDev integer gDarkOffsetNumPts rDarkOffsetNumPts integer gNumSatFeat rNumSatFeat The number of saturated features on the microarray per channel float gLocalBGInlierAve rLocalBGlnlierAve The average of all inlier local backgrounds float gLocalBGlnlierSDev rLocalBGlnlierSDev The standard deviation of all inlier local backgrounds integer gLocalBGlnlierNum rLocalBGInlierNum The number of inlier local backgrounds float gGlobalBGinlierAve rGlobalBGInlierAve The average of all inliers used in background estimation for the selected global background subtraction method or the average of all inlier local backgrounds if the local background subtraction method is selected after global background adjustment is applied if selected float gGlobalBGInlierSDev rGlobalBGInlierSDev The standard deviation of all inliers used in background estimation for the selected global background subtraction method or the standard deviation of all inlier local backgrounds if the local background subtraction method is selected integer gGlobalBGinlierNum rGlobalBGInlierNum The number of all inliers used in background estimation for the selected global background subtraction method or the number of all inlier loc
7. al backgrounds if the local background subtraction method is selected 162 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 18 Stats results contained in the text output file STATS table Type Stats Green Channel Stats Red Channel Description integer gNumFeatureNonUnifOL rNumFeatureNonUnifOL The number of features that are flagged as non uniformity outliers integer gNumPopnOL rNumPopnOL The number of features that are flagged as population outliers integer gNumNonUnifBGOL rNumNonUnifBGOL The number of local background regions that are flagged as non uniformity outliers integer gNumPopnBGOL rNumPopnBGOL The number of local background regions that are flagged as population outliers float gOffsetUsed rOffsetUsed Software estimated scanner offset float gGlobalFeatInlierAve rGlobalFeatinlierAve Average of all inlier features float gGlobalFeatInlierSDev rGlobalFeatInlierSDev Standard deviation of all inlier features float gGlobalFeatInlierNum rGlobalFeatInlierNum Number of all inlier features integer gNumNegBGSubFeat rNumNegBGSubFeat Number of background subtracted features with negative signals float gNegCtriSigLevel rNegCtrlSigLevel Average of all negative controls used in background subtraction integer gNegCtrlSeqUsed rNegCtriSeqUsed Bit mask indicating probe IDs of the negative control groups used for computation of negative control signal level in background subtraction float gS
8. er_BGCTerm OutlierFlagger_ConflntPValue OutlierFlagger_PopnOLOn 1 OutlierFlagger_lORatio OutlierFlagger_MinPopulation BGSubtractor BGSubtractor_Version Applies to feature specifies the variance due to the Poisson distributed noise Applies to feature specifies variance due to background noise of the scanner slide glass and other signal independent sources Applies to background specifies the intensity dependent variance and is set to the square of the CV Applies to background specifies the variance due to the Poisson distributed noise Applies to background specifies variance due to background noise of the scanner slide glass and other signal independent sources p value at which statistical significance for polynomial outlier flagging is established Population Outlier flagging turned on Population Outlier flagging turned off The boundary conditions for conducting box plot analysis to isolate population outliers Minimum number of replicates to turn on population outlier flagging GUID of BG subtractor algorithm Version of BGSubtractor algorithm Agilent G2567AA Feature Extraction Software v 7 5 User Manual 157 6 Settings and Results Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Description integer float float integer integer integer integer integer BGSubtractor_BGSubMethod BGSubtrac
9. integer Row Feature location row integer Col Feature location column integer Start Start position of the probe sequence text Sequence The probe sequence as specified in the design file integer ProbeUID Unique integer for each unique probe in a design integer ControlType Feature control type 0 Control type none 1 Positive control 1 Negative control 10000 Deletion control 20000 Not probe text ProbeName An Agilent assigned identifier for the probe synthesized on the microarray text GeneName This is an identifier for the gene for which the probe provides expression information The target sequence identified by the systematic name is normally a representative or consensus sequence for the gene Agilent G2567AA Feature Extraction Software v 7 5 User Manual 165 Settings and Results Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description text text float float float float SystematicName Description PositionX PositionY LogRatio base 10 LogRatioError 1000 PValueLogRatio This is an identifier for the target sequence that the probe was designed to hybridize with Where possible a public database identifier is used e g TAIR locus identifier for Arabidopsis Systematic name is reported ONLY if Gene name and Systematic name are different Found coordinates of the feature centroid in pixels l
10. kground difference is significant To view variables used in the t test see Table 29 on page 214 170 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description float Boolean Boolean float Boolean float float integer gPValFeatEqBG glsWellAboveBG gSpatialDetrendlsin FilteredSet gSpatialDetrend SurfaceValue IsUsedBGAdjust gBGUsed gBGSDUsed DelCtriFeatNum rPValFeatEqBG rlsWellAboveBG rSpatialDetrendlsIin FilteredSet rSpatialDetrend SurfaceValue rBGUsed rBGSDUsed 1 Feature used 0 Feature not used gBGSubSignal gMeanSignal gBGUsed P value from t test of significance between g r Mean signal and g r background selected by user Boolean flag indicating if a feature is WellAbove Background or not Feature passes g r lsPosAndSignif and additionally the g r BGSubSignal is greater than 2 6 g r BG_SD Set to true for a given feature if it is part of the filtered set used to detrend the background This featire is considered part of the locally weighted lowest x of features as defined by the DetrendLowPassPercentage Value of the smoothed surface calculated by the Spatial detrend algorithm A Boolean used to flag features used for computation of global BG offset Background used to
11. nOL g r lsFeatPopnOL Boolean flag indicating if a feature is a 1 indicates Feature Population Outlier or not Probes with is a population replicate features on a microarray are outlier in g r examined using population statistics A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using a multiplier 1 42 times the interquartile range i e IQR of the population boolean glsBGPopnOL rlsBGPopnOL g r IsBGPopnOL 1 The same concept as above but for indicates local background background is a population outlier in g r boolean IsManualFlag float gBGSubSignal rBGSubSignal gBGSubSignal Background subtracted signal To view gMeanSignal the values used to calculate this variable gBGUsed using different background signals and settings of spatial detrend and global background adjust see Table 29 on page 214 float gBGSubSigError rBGSubSigError Propagated standard error as computed on net g r background subtracted signal float BGSubSigCorrelation Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space Boolean glsPosAndSignif rlsPosAndSignif g r isPosAndSignif Boolean flag established via a 2 sided 1 indicates t test indicates if the mean signal of a Feature is positive feature is greater than the corresponding and significant background selected by user and if this above bac
12. og REDsignal GREENsignal per feature processed signals used If SURROGATES are turned off then if DyeNormRedSig lt 0 0 amp DyeNormGreenSig gt 0 0 if DyeNormRedSig gt 0 0 amp DyeNormGreenSig lt 0 0 if DyeNormRedSig lt 0 0 amp DyeNormGreenSig lt 0 0 If SURROGATES are turned off then if DyeNormRedSig lt 0 0 OR DyeNormGreenSig lt 0 0 IF SURROGATES are turned on then LogRatioError error of the log ratio calculated according to the error model chosen Significance level of the Log Ratio computed for a feature 166 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description float gSurrogateUsed rSurrogateUsed non zero value The green red surrogate value used Green red surro gate value used 0 No surrogate value used boolean glsFound rlsFound 1 IsFound A boolean used to flag found strong 0 IsNotFound features The flag is applied independently in each channel A feature is considered found if the calculated spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid NOTE IsFound was previously termed IsStrong float SpotRadiusX Radius of the spot X axis when Calculate Spot Size and WholeSpot method are selected float SpotRadiusY Radius of the spo
13. orrection has been applied based upon the LOWESS curve float DyeNormUnitWeightedRMS Unit weighted RMS correction metric Metric that indicates how much correction has been applied based upon the LOWESS curve float AllColorPrentSat The percentage of features that are saturated in both the green AND red channels float AnyColorPrentSat The percentage of features that are saturated in either the green or red channel float AnyColorPrentFeatNonUnifOL The percentage of features that are feature non uniformity outliers in either channel float AnyColorPrentBGNonUnifOL The percentage of local backgrounds that are non uniformity outliers in either channel float AnyColorPrentFeatPopnOL The percentage of features that are population outliers in either the green or red channel float AnyColorPrentBGPopnOL The percentage of local backgrounds that are population outliers in either channel float TotalPrentFeatOL The percentage of non control features that are feature non uniformity outliers in either the green or red channel or are saturated in both channels 164 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Feature results FEATURES Settings and Results 6 The bottom section of the text file gives descriptions of the results for each feature Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description integer FeatureNum Feature number
14. patialDetrendRMS Fit rSpatialDetrendRMS Fit Root mean square RMS of the fitted data points obtained from the Loess algorithm This gives an idea of the curvature of the surface fit float gSpatialDetrendRMS Filtered rSpatialDetrendRMS Approximate residual from the surface fit minus Fit Filtered minus Fit float gSpatialDetrendSurfaceArea rSpatialDetrendSurface Normalized area the fitted surface area divided by Area the projected area on the microarray also gives an idea of the curvature of the surface gradient Agilent G2567AA Feature Extraction Software v 7 5 User Manual 163 6 Settings and Results Table 18 Stats results contained in the text output file STATS table Type Stats Green Channel Stats Red Channel Description float gSpatialDetrendVolume rSpatialDetrendVolume Sum of the intensities of the surface area minus the offset The offset is calculated as the volume under the flat surface parallel to the glass slide passing through the minimum intensity point of the fitted surface This number total volume offset is normalized by the area of the microarray float gSpatialDetrendAveFit rSpatialDetrendAveFit Describes the average intensity of the surface gradient float gBGAdjust rBGAdjust Global Background correction offset applied float gLinearDyeNormFactor rLinearDyeNormFactor Global dye norm factor float DyeNormDimensionlessRMS Dimensionless RMS correction metric Metric that indicates how much c
15. rName Computer Name on which Feature Extraction was run text FeatureExtractor_ExtractionTime Time stamp which is applied at the beginning of Feature Extraction text SpotFinder Software component ID GUID of the Find Spots algorithm text SpotFinder_Version Version of Find Spots algorithm 154 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Options Description integer SpotFinder_NumRows Number of rows in the microarray integer SpotFinder_NumCols Number of columns in the microarray float SpotFinder_DevLimit The maximum offset in both x and y directions that any feature can deviate from its nominal spot center and still be reported as Found The value is reported in pixels float SpotFinder_ROIW The principal grid is determined by the SpotFinder_ROIH overall size rows columns of the microarray this is further segmented into smaller regions of interest ROIs about a particular nominal spot location within which spotfinder tries to determine the true center of a spot The parameters refer to the width and height of this ROI float SpotFinder_NomSpotWidth Spot parameters extracted from the design SpotFinder_NomSpotHeight file or grid file or calculated when Calculate Spot Size selected values reported in pixels text CornerMethod Auto Find Corners The corners were automatically fo
16. size value for WholeSpot method an averaged measure float CalcSpotStats_CookieHeight Cookie height pixels based on nominal spot size Same as for Cookie Width float CalcSpotStats_BGInnerWidth Outer bounds of the exclusion zone width pixels based on nominal spot size Same as for Cookie Width float CalcSpotStats_BGInnerHeight Outer bounds of the exclusion zone height pixels based on nominal spot size Same as for Cookie Width float CalcSpotStats_BGOuterWidth Background radius value independent of SpotAnalysis method float CalcSpotStats_BGOuterHeight Background radius value independent of SpotAnalysis method text OutlierFlagger Software component ID of Outlier Flagger algorithm text OutlierFlagger_Version Version of Outlier Flagger algorithm integer OutlierFlagger_NonUnifOLOn 1 NonUniformity Outlier flagging turned on 0 NonUniformity Outlier flagging turned off float OutlierFlagger_FeatATerm Applies to feature specifies the intensity dependent variance and is set to the square of the CV 156 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Options Description float float float float float float integer float integer text text OutlierFlagger_FeatBTerm OutlierFlagger_FeatCTerm OutlierFlagger_BGATerm OutlierFlagger_BGBTerm OutlierFlagg
17. t Y axis when Calculate Spot Size and WholeSpot method are selected boolean UsedAveRadiusfor 1 Average radius This radius is used if a spot is extremely WholeSpot used for WholeSpot noisy or is essentially empty analysis 0 Exact contour determined and used for WholeSpot analysis float gProcessedSignal rProcessedSignal Dye normalized signal after surrogate algorithm per channel used for computation of log ratio float gProcessedSigError rProcessedSigError Standard error of propagated feature signal per channel Agilent G2567AA Feature Extraction Software v 7 5 User Manual 167 6 Settings and Results Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description integer integer integer float float float integer float gNumPixOLHi gNumPixOLLo gNumPix gMeanSignal gMedianSignal gPixSDev gBGNumPix gBGMeanSignal rNumPixOLHi rNumPixOLLo rNumPix rMeanSignal rMedianSignal rPixSDev rBGNumPix rBGMeanSignal Number of outlier pixels per feature with intensity gt upper threshold set via the pixel outlier rejection method The number is computed independently in each channel These pixels are omitted from all subsequent calculations Number of outlier pixels per feature with intensity lt lower threshold set via the pixel outlier rejection method The number is comp
18. text output file FEPARAMS table Type Parameters Options Description integer BGSubtractor_DetrendLowPass Specifies size of the square window by the Window number of rows and columns The specified percentage of low intensity features is selected from this window size integer BGSubtractor_DetrendLowPass The increment in number of features by Increment which the above window is shifted horizontally and vertically on the microarray float BGSubtractor_DetrendNeighborhood Specifies the fraction of total number of Size neighborhood data points that will be weighted for linear regression during surface fitting for each data point text DelCtrl Software component ID GUID of deletion control algorithm text DelCtrl_Version Version of deletion control algorithm text DyeNorm GUID of DyeNorm algorithm text DyeNorm_Version Version of DyeNorm algorithm integer DyeNorm_SelectMethod Method for selecting features used for measurement of dye bias 4 All significant non control non outlier features 5 List of normalization genes 6 Rank Consistency Filter Boolean DyeNorm_IlsBGPopnOLOn 1 0N This setting is found in the DyeNorm tab If 2 OFF the check box is marked the software excludes any features from the dye normalization set if the local backgrounds associated with those features have been flagged as population outliers in either channel The default recommendation is OFF Agilent G2567AA Feature Extraction Software v 7 5 User Manual 1
19. tlier in g r g r IsBGNonUnifOL 1 indicates Local background is a non uniformity outlier in g r Median local background signal local to corresponding feature computed per channel inlier pixels Standard deviation of all inlier pixels per Local BG of each feature computed independently in each channel Total number of saturated pixels per feature computed per channel Boolean flag indicating if a feature is saturated or not A feature is saturated IF 50 of the pixels in a feature are above the saturation threshold Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space The covariance of two features measures their tendency to vary together i e to co vary In this case it is a cumulative quantitation of the tendency of pixels belonging to a particular feature in Red and Green spaces to co vary The same concept as above but in case of background Boolean flag indicating if a feature is a NonUniformity Outlier or not A feature is non uniform if the pixel noise of feature exceeds a threshold established for a uniform feature The same concept as above but for background Agilent G2567AA Feature Extraction Software v 7 5 User Manual 169 6 Settings and Results Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description boolean glsFeatPopnOL rlsFeatPop
20. tor_MaxPVal BGSubtractor_WellAboveMulti BGSubtractor_BackgroundCorrectionOn BGSubtractor_BgCorrectionOffset BGSubtractor_SpatialDetrendOn BGSubtractor_DetrendLowPassFilter BGSubtractor_DetrendLowPass Percentage Either minimum feature or minimum local background across the microarray for background subtraction global method Average of local backgrounds for background subtraction global method Average of negative controls for background for background subtraction global method Local background corresponding to each feature for background subtraction local method Minimum feature across the microarray for background subtraction global method No background subtraction The p value at which a feature is determined to be statistically significant above background The number of standard deviations above background at which the feature is flagged as well above background Globally adjust background turned on Globally adjust background turned off Value with which to center the signals of the low signal features pad value Spatial detrend turned on Spatial detrend turned off Low pass filter used Low pass filter not used Specifies percentage of features based on the lowest intensity probes in each window that will be used to fit the surface 158 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 17 List of parameters and options contained within the
21. und Manual Lock Corners The corners were selected manually and locked by the user Manual no lock The corners were selected manually and corners allowed to be refined by the software float SpotFinder_Baseline Baseline intensity used for auto find corners float SpotFinder_AutoFindTh Threshold intensity used for auto corner finding float CornerUL_x x y coordinates of the corners of the final CornerUL_y grid with top left hand side of the analysed CornerUR_x image set as origin 0 CornerUR_y CornerLL_x CornerLL_y text CalcSpotStats GUID of CalcSpotStats algorithm text CalcSpotStats_Version Version of CalcSpotsStats algorithm Agilent G2567AA Feature Extraction Software v 7 5 User Manual 155 6 Settings and Results Table 17 List of parameters and options contained within the text output file FEPARAMS table Type Parameters Options Description integer CalcSpotStats_RejectMethod 0 Pixel Outlier Rejection turned off 2 Standard Deviation based 3 Interquartile Range based float CalcSpotStats_StatBoundFeat Multiplier parameters for feature outlier rejection method as selected above float CalcSpotStats_StatBoundBG Multiplier parameters for background outlier rejection method as selected above Boolean CalcSpotStats_CalculateSpotSize 0 option OFF Option to calculate the spot size found in 1 option ON SpotAnalyzer tab must be ON for WholeSpot method float CalcSpotStats_CookieWidth Cookie width pixels based on nominal spot
22. uted independently in each channel These pixels are omitted from all subsequent calculations NOTE The pixel outlier method is the ONLY step that removes data in Feature Extraction Total number of pixels used to compute feature statistics ie total number of inlier pixels per spot same in both channels Raw mean signal of feature in green red channel inlier pixels Raw median signal of feature in green red channel inlier pixels Standard deviation of all inlier pixels per feature this is computed independently in each channel Total Number of pixels used to compute Local BG statistics per spot ie total number of BG inlier pixels same in both channels Mean local background signal local to corresponding feature computed per channel inlier pixels 168 Agilent G2567AA Feature Extraction Software v 7 5 User Manual Settings and Results 6 Table 19 Feature results contained in the output text file FEATURES table Types Features Green Features Red Options Description float float integer boolean float float boolean boolean gBGMedianSignal gBGPixSDev gNumSatPix glsSaturated PixCorrelation BGPixCorrelation glsFeatNonUnifOL glsBGNonUnifOL rBGMedianSignal rBGPixSDev rNumSatPix rlsSaturated rlsFeatNonUnifOL rlsBGNonUnifOL 1 Saturated or 0 Not saturated g r lsFeatNonUnifOL 1 indicates Feature is a non uniformity ou
23. versal error model chosen by you or by software If the g r PerfMatchSignal is positive and significant versus its g r DelCtrlSignal a ratio is calculated between the PerfMatch net signal and the DelCtrl net signal else the ratio is set to 1 The g r net signal is equal to the g r BGSubSignal if the signal passes g r WellAboveBG else the g r net signal is equal to 2 6 g r BGSDUsed A boolean flag which indicates if a feature is used to measure dye bias The dye normalized signal in the indicated channel The standard error associated with the dye normalized signal Dye normalized red and green pixel correlation Indicates the error model that you chose for Feature Extraction or that the software uses if you have chosen the Most Conservative option A signal to noise parameter used to calculate p value calculated differently depending on error model chosen Agilent G2567AA Feature Extraction Software v 7 5 User Manual 173
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