[BioC] input agilent single-channel data (using limma package)

[Gordon K Smyth]

Dear Liuyang,

Your Agilent feature extraction files don't include mean signals for some 
reason, only median signals.  Hence you must use:

   dat <- read.mimages(files, source="agilent.median", green.only=TRUE)

Note also the use of green.only to tell limma that this is single channel 
data, with green channel only.

Best wishes
Gordon

> Date: Wed, 21 Sep 2011 12:25:14 +0800
> From: liuyang zhao <wszly626 at gmail.com>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] a question about input agilent single-channel data to
> 	R ( using limma package). Thanks for your kind help.
>
> Dear bioconductor,
>
>     I input agilent single-channel data to R using the code as follow?
>
>> library(limma)
>> dat<-read.maimages(files=dir(), columns=list(+ G = "gMeanSignal", Gb =
> "gBGMedianSignal",+ R = "gMeanSignal", Rb = "gBGMedianSignal"))
>
> i have successfully  input the affy .cel data  to R,but i don't why it not
> using Agilent data.
>
> Would you kind enough to  tell me the right code to input the agilent to R?
> thanks!
>
> Here is a sample of  agilent data.
>
> Thanks for your reading my message.
>
> Best wishes,
>
> Liuyang Zhao
> Chongqing Medical University
> China
> -------------- next part --------------

> 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 gNegCtrlAve! NetSig 
> 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 gXDRLowPMTSlope 
> gXDRLowPMTIntercept 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

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