I was doing QC analysis in aroma in R on HuEx chip but got an error
while trying to plot NUSE.
ylim contains NA.
I'm running R 2.10(32bit) on a windows 7(64bit).
my command:
library(aroma.affymetrix)
verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType(chipType)
print(cdf)
cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
bc <- RmaBackgroundCorrection(cs)
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
csN <- process(qn, verbose=verbose)
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
qamTr <- QualityAssessmentModel(plmTr)
plotNuse(qamTr)
plotRle(qamTr)
<<End of command
I was able to run the previous on U95A data and Plus 2 data. Also, in
the past I was able to run that on HuEx data.
The cdf file I'm using is binary and used multiples ones (HuEx-1_0-
st-
v2,core,A20071112,EP.cdf, HuEx-1_0-st-
v2,control,A20071112,EP.cdf, HuEx-1_0-st-
v2,extended,A20071112,EP.cdf etc offered on Elizabeth's Column
http://groups.google.com/group/aroma-affymetrix/web/affymetrix-defined-transcript-clusters?pli=1
)
Could you please point me how to fix this problem?
Thanks in advance
--
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