Question: Pulling significant gene ids from beadarray data
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gravatar for Johnstone, Alice
12.3 years ago by
Johnstone, Alice410 wrote:
I have been analysing my Illumina data from rat ref12 using beadarray and the summary data. I have managed to get a list of significantly different probes, but am at a loss as to how to get the gene info this corresponds to. The ExpressionSetIllumina object doesn't contain any annotation data, neither the ProbeID or the TargetID appear to be incorporated following the code in the vignette (march 26 2007). Is there a way to include this to ensure I am following the right probe? Then is there a way to get the gene information directly to R, such as when using the lumi package and nuID etc? Any help gratefully appreciated! Alice Johnstone PhD Candidate Institute of Environmental Science and Research Ltd Kenepuru Science Centre 34 Kenepuru Drive PO Box 50-348 Porirua New Zealand Tel: + 64 4 914-0717 Fax: + 64 4 914-0770 dataFile="ROD-AJ-BeadStudioV2_Sample_Probe_Profile.csv" qcFile="ControlGeneProfile.csv" sampleSheet="sampleSheet.csv" BSData<-readBeadSummaryData(dataFile,qcFile=qcFile,sampleSheet=sampleS he et, header=TRUE,skip=7,columns=list(exprs="AVG_Signal",BeadStDev="BEAD_STD EV ", NoBeads="Avg_NBEADS"),qc.columns=list(exprs="AVG.Signal",Detection="De te ction"), qc.skip=0,qc.sep=",",sep=",") > exprs(BSData)[1:10,1:2] SAL SAL.1 1 151.8 151.2 2 142.6 133.4 3 143.6 151.0 4 135.6 138.2 5 149.5 153.6 6 133.1 155.1 7 141.2 157.4 8 144.2 135.4 9 168.0 132.7 10 126.5 144.7 > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] "grid" "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: beadarray beadarraySNP quantsmooth lodplot quantreg SparseM affy affyio geneplotter "1.4.0" "1.2.0" "1.2.0" "1.1" "4.08" "0.73" "1.14.2" "1.4.1" "1.14.0" lattice annotate Biobase limma "0.15-11" "1.14.1" "1.14.1" "2.10.5"
ADD COMMENTlink written 12.3 years ago by Johnstone, Alice410
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