Hi,
there are probably more output from the error, or ? If so, could you
please provide us with that one? Also, whenever you get an error, is
it is always helpful to report output of traceback() [see email
footer].
What's your sessionInfo()?
/Henrik
On Wed, Feb 24, 2010 at 7:29 PM, zaid <z...@genomedx.com> wrote:
> 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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