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Johnstone, Alice
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410
@johnstone-alice-2290
Last seen 10.3 years ago
Hi
Stuck at the beginning(!) reading in my Illumina summary data using:
> dataFile="ROD-AJ-BeadStudioV2_Sample_Probe_Profile.csv"
> qcFile="ControlGeneProfile.txt"
> sampleSheet="sampleSheet.txt"
>
BSData<-readBeadSummaryData(dataFile,qcFile=qcFile,sampleSheet=sampleS
he
et,
+
header=TRUE,ProbeID="TargetID",skip=7,columns=list(exprs="AVG_Signal",
Be
adStDev="BEAD_STDEV",
+
NoBeads="Avg_NBEADS"),qc.columns=list(ControlID="TargetID",exprs="AVG.
Si
gnal",Detection="Detection"),
+ qc.sep=",",sep=",")
Did not find a slot called : ControlID
In the help for readBeadSummaryData it has a ControlID slot for the
qcFile listed, am I missing something?
> 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"
[7] "datasets" "methods" "base"
other attached packages:
beadarray beadarraySNP quantsmooth lodplot quantreg
SparseM
"1.4.0" "1.2.0" "1.2.0" "1.1" "4.08"
"0.73"
affy affyio geneplotter lattice annotate
Biobase
"1.14.2" "1.4.1" "1.14.0" "0.15-11" "1.14.1"
"1.14.1"
limma
"2.10.5"
Thanks
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