Dear mailing list, I encountered strange problems while loading a Agilent human 4x44k G4112F array. This data was pulled from NCBI GEO GSM648499. It turned out, that the data was produced with Agilent Feature Exractor version 10.7.. I first tried to read it in with read.AgilentFE from the package Agi4x44kPreProcess. It stopped with specified columns not found. Then I tried directly using limma's read.maimages. Now I got an RGlist, however I want to use Agi4x44PreProcess. So I had a look at the code. Indeed it was lookiong for columns, that are NOT in my data file. I modified the code to not look for columns noot present, however I wasn't successful. It turned out that read.AgilentFE depended on Chro_Coord and Sequence! Please give me a hand! I have written down the first few lines of my Agi raw data file: TYPE text text text integer text float float text integer text text integer integer integer integer float float float float float float text text text text text text text text text text text integer integer integer FEPARAMS Protocol_Name Protocol_date Scan_ScannerName Scan_NumChannels Scan_Date Scan_MicronsPerPixelX Scan_MicronsPerPixelY Scan_OriginalGUID Scan_NumScanPass Grid_Name Grid_Date Grid_NumSubGridRows Grid_NumSubGridCols Grid_NumRows Grid_NumCols Grid_RowSpacing Grid_ColSpacing Grid_OffsetX Grid_OffsetY Grid_NomSpotWidth Grid_NomSpotHeight Grid_GenomicBuild FeatureExtractor_Barcode FeatureExtractor_Sample FeatureExtractor_ScanFileName FeatureExtractor_ArrayName FeatureExtractor_ScanFileGUID FeatureExtractor_DesignFileName FeatureExtractor_ExtractionTime FeatureExtractor_UserName FeatureExtractor_ComputerName FeatureExtractor_Version FeatureExtractor_IsXDRExtraction FeatureExtractor_ColorMode FeatureExtractor_QCReportType DATA GE1_107_Sep09 (Read Only) 29-Sep-2009 12:35 Agilent Technologies Scanner G2505C US94000320 1 05-07-2010 12:01:53 5 5 9ceee5f3-441a-4c83-838c-44fc6ed56037 1 014850_D_F_20100430 30-Apr-2010 00:00 1 1 532 85 73.3235 63.5 0 36.6617 65 65 hg19:GRCh37:Feb2009 251485054565_1_4 D:\100507kuma_M,H GE (mae)\\US94000320_251485054565_S01.tif US94000320_251485054565_S01 2d3d94a7-3aff-4a36-8108-be5f8c3127ca 014850_D_F_20100430.xml 07-May-2010 13:31:12 Administrator DATASYSTEM01 10.7.3.1 0 0 0 * TYPE float float float integer integer float float float integer float float float integer float float integer integer integer integer integer float float float integer float float float float float integer integer float float float float float integer float float float float integer float float float float float integer float float float float float float float integer float integer float float float float integer float float float float text float float float float float float float float float float float float float float float float float float float float float integer integer integer integer float integer text integer boolean float float boolean float boolean float boolean float boolean float boolean float boolean float boolean float boolean float boolean float boolean STATS gDarkOffsetAverage gDarkOffsetMedian gDarkOffsetStdDev gDarkOffsetNumPts gSaturationValue gAvgSig2BkgeQC gAvgSig2BkgNegCtrl gRatioSig2BkgeQC_NegCtrl gNumSatFeat gLocalBGInlierNetAve gLocalBGInlierAve gLocalBGInlierSDev gLocalBGInlierNum gGlobalBGInlierAve gGlobalBGInlierSDev gGlobalBGInlierNum gNumFeatureNonUnifOL gNumPopnOL gNumNonUnifBGOL gNumPopnBGOL gOffsetUsed gGlobalFeatInlierAve gGlobalFeatInlierSDev gGlobalFeatInlierNum AnyColorPrcntFeatNonUnifOL AnyColorPrcntBGNonUnifOL AnyColorPrcntFeatPopnOL AnyColorPrcntBGPopnOL TotalPrcntFeatOL gNumNegBGSubFeat gNonCtrlNumNegFeatBGSubSig gSpatialDetrendRMSFit gSpatialDetrendRMSFilteredMinusFit gSpatialDetrendSurfaceArea gSpatialDetrendVolume gSpatialDetrendAveFit gNonCtrlNumSatFeat gNonCtrl99PrcntNetSig gNonCtrl50PrcntNetSig gNonCtrl1PrcntNetSig gNonCtrlMedPrcntCVBGSubSig gCtrleQCNumSatFeat gCtrleQC99PrcntNetSig gCtrleQC50PrcntNetSig gCtrleQC1PrcntNetSig geQCMedPrcntCVBGSubSig geQCSig2BkgLow2 gNegCtrlNumInliers gNegCtrlAveNetSig gNegCtrlSDevNetSig gNegCtrlAveBGSubSig gNegCtrlSDevBGSubSig gAveNumPixOLLo gAveNumPixOLHi gPixCVofHighSignalFeat gNumHighSignalFeat AddErrorEstimateGreen TotalNumFeatures ROIHeight ROIWidth CentroidDiffX CentroidDiffY NumFoundFeat MaxNonUnifEdges MaxSpotNotFoundEdges gMultDetrendRMSFit gMultDetrendSurfaceAverage eQCLowSigName2 eQCOneColorLogLowSignal eQCOneColorLogLowSignalError eQCOneColorLogHighSignal eQCOneColorLinFitLogLowConc eQCOneColorLinFitLogLowSignal eQCOneColorLinFitLogHighConc eQCOneColorLinFitLogHighSignal eQCOneColorLinFitSlope eQCOneColorLinFitIntercept eQCOneColorLinFitRSQ eQCOneColorSpikeDetectionLimit gNonCtrl50PrcntBGSubSig gCtrleQC50PrcntBGSubSig gMedPrcntCVProcSignal geQCMedPrcntCVProcSignal gOutlierFlagger_Auto_FeatB_Term gOutlierFlagger_Auto_FeatC_Term gOutlierFlagger_Auto_BgndB_Term gOutlierFlagger_Auto_BgndC_Term OutlierFlagger_FeatChiSq OutlierFlagger_BgndChiSq GriddingStatus IsGoodGrid NumGeneNonUnifOL TotalNumberOfReplicatedGenes gPercentileIntensityProcessedSignal ExtractionStatus QCMetricResults gNonCtrlNumWellAboveBG GridHasBeenOptimized gNegCtrlSpread Metric_IsGoodGrid Metric_IsGoodGrid_IsInRange Metric_AnyColorPrcntFeatNonUnifOL Metric_AnyColorPrcntFeatNonUnifOL_IsInRange Metric_gNegCtrlAveNetSig Metric_gNegCtrlAveNetSig_IsInRange Metric_gNegCtrlAveBGSubSig Metric_gNegCtrlAveBGSubSig_IsInRange Metric_gNegCtrlSDevBGSubSig Metric_gNegCtrlSDevBGSubSig_IsInRange Metric_gSpatialDetrendRMSFilteredMinusFit Metric_gSpatialDetrendRMSFilteredMinusFit_IsInRange Metric_gNonCntrlMedCVProcSignal Metric_gNonCntrlMedCVProcSignal_IsInRange Metric_gE1aMedCVProcSignal Metric_gE1aMedCVProcSignal_IsInRange Metric_absGE1E1aSlope Metric_absGE1E1aSlope_IsInRange Metric_DetectionLimit Metric_DetectionLimit_IsInRange DATA 8.24619 8.24619 1.84518 0 778064 2507.05 1.08752 2305.3 0 23.0119 31.2581 2.1342 43748 31.2581 2.1342 43748 40 129 9 1267 8.24619 5143.71 22514.3 44850 0.0888593 0.0199933 0.286571 2.81462 0.0899115 5668 4703 1.24945 2.4057 1.00119 3.11615 34.1486 0 104217 154.705 22.2069 11.4119 0 375617 2641.25 23.0236 10.3921 1.0353 146 24.0152 2.21446 -1.79617 1.784 0.465267 1.03585 0.119728 7188 2.4057 45015 4.35314 7.61791 1.38897 1.12018 36823 0.0037594 0.288235 0.0962958 1.00214 (+)E1A_r60_3 0.0154106 0.283794 5.89102 0.495325 0.334397 6.25138 5.73138 0.937618 -0.130028 0.992794 1.17372 128.699 2613.91 3.63153 3.31337 611.579 59.1813 88.4118 46.7179 1.94937 2.39892 0 1 36 41000 1368.3 0 ExtractionInRange 30563 0 6.43395 1 1 0.088859 1 24.0152 1 -1.79617 1 1.784 1 2.4057 1 3.63153 1 3.31337 1 0.937618 1 1.17372 1 * TYPE integer integer integer integer integer text text float float float float float float float boolean boolean boolean boolean boolean boolean float boolean boolean float float FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY gProcessedSignal gProcessedSigError gMedianSignal gBGMedianSignal gBGPixSDev gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gIsPosAndSignif gIsWellAboveBG SpotExtentX gBGMeanSignal DATA 1 1 1 260 1 GE_BrightCorner GE_BrightCorner 9814.49 280.468 1.609650e+005 1.609650e+004 121087 24 6.313175e+000 0 0 0 0 1 0 122096 1 1 57.5363 24.1297 * <http: www.ncbi.nlm.nih.gov="" geo="" query="" acc.cgi?acc="GSM648499">* [[alternative HTML version deleted]]