[BioC] AgiMicroRna for new Agilent Chip format - columns gTotalGeneSignal and gTotalProbeSignal missing
Constanze [guest]
guest at bioconductor.org
Sat Feb 23 22:10:01 CET 2013
Dear All,
i have Agilent gene expression data (SurePrint G3 Human Gene Expression 8x60K v2 Microarray; chip type 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
If AgiMicroRna is not adapted for this type of data, are there any good alternatives?
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
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