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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}