Agilent Chip G4858A-039494: columns gTotalGeneSignal, gTotalProbeSignal missing for AgiMicroRna
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Dear All, i recently got some Agilent (G4858A-039494) data. Feature extraction was done setting TextOutPkgType="Full". I want to rma-normalize this data but realize i'm missing two of the columns required by readMicroRnaAFE in AgiMicroRna : gTotalGeneSignal and gTotalProbeSignal. Here is the list of features i have on the chip: FEATURES FeatureNum Row Col accessions chr_coord SubTypeMask SubTypeName Start Sequence ProbeUID ControlType ProbeName GeneName SystematicName Description PositionX PositionY gSurrogateUsed gIsFound gProcessedSignal gProcessedSigError gNumPixOLHi gNumPixOLLo gNumPix gMeanSignal gMedianSignal gPixSDev gPixNormIQR gBGNumPix gBGMeanSignal gBGMedianSignal gBGPixSDev gBGPixNormIQR gNumSatPix gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gBGSubSigError gIsPosAndSignif gPValFeatEqBG gNumBGUsed gIsWellAboveBG gBGUsed gBGSDUsed ErrorModel gSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue SpotExtentX SpotExtentY gNetSignal gMultDetrendSignal gProcessedBackground gProcessedBkngError IsUsedBGAdjust gInterpolatedNegCtrlSub gIsInNegCtrlRange gIsUsedInMD I'd appreciate any suggestions on how to treat this data set. Thanks very much, Constanze -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=de_CH.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_CH.UTF-8 LC_COLLATE=de_CH.UTF-8 [5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_2.6.0 affycoretools_1.28.0 KEGG.db_2.7.1 [4] GO.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.18.4 preprocessCore_1.18.0 affy_1.34.0 [10] limma_3.12.3 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 [4] BiocInstaller_1.4.9 biomaRt_2.12.0 Biostrings_2.24.1 [7] Category_2.22.0 gcrma_2.28.0 genefilter_1.38.0 [10] GOstats_2.22.0 graph_1.34.0 grid_2.15.1 [13] GSEABase_1.18.0 IRanges_1.14.4 lattice_0.20-10 [16] RBGL_1.32.1 RCurl_1.95-3 splines_2.15.1 [19] stats4_2.15.1 survival_2.36-14 tools_2.15.1 [22] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
GO AgiMicroRna GO AgiMicroRna • 1.0k views
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