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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