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Andreas Heider
▴
340
@andreas-heider-4538
Last seen 9.8 years ago
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">*
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