Error:
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
$yaxs) :
NAs not allowed in 'ylim'
On Feb 24, 10:19 am, zaid <z...@genomedx.com> wrote:
> I was doing QC analysis in aroma in R on HuEx chip but got an error
> while trying to plot NUSE.
> ylim contains NA.
>
> I'm running R 2.10(32bit) on a windows 7(64bit).
>
> my command:
> library(aroma.affymetrix)
> verbose <- Arguments$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
> Columnhttp://groups.google.com/group/aroma-affymetrix/web/affymetrix-define...
> )
>
> Could you please point me how to fix this problem?
>
> Thanks in advance
--
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