>traceback()
8: plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs)
7: bxp(bxpStats, ylim = ylim, outline = outline, las = las, ...)
6: plotBoxplotStats.list(stats, main = main, ylab = ylab, ...)
5: plotBoxplotStats(stats, main = main, ylab = ylab, ...)
4: plotBoxplot.ChipEffectSet(ces, type = "RLE", ...)
3: plotBoxplot(ces, type = "RLE", ...)
2: plotRle.QualityAssessmentModel(qamTr)
1: plotRle(qamTr)
>qamTr
QualityAssessmentModel:
Name: tissues
Tags: RBC,QN,RMA,merged,QC
Path: qcData/tissues,RBC,QN,RMA,merged,QC/HuEx-1_0-st-v2
Chip-effect set:
ExonChipEffectSet:
Name: tissues
Tags: RBC,QN,RMA,merged
Path: plmData/tissues,RBC,QN,RMA,merged/HuEx-1_0-st-v2
Platform: Affymetrix
Chip type: HuEx-1_0-st-v2,monocell
Number of arrays: 2
Names: S370-A-HuEx-1_0-st-v2-01-1 (S09-13138), S371-A-HuEx-1_0-st-
v2-01-1 (S09-07848)
Time period: 2010-02-24 10:28:31 -- 2010-02-24 10:28:31
Total file size: 5.43MB
RAM: 0.01MB
Parameters: (probeModel: chr "pm", mergeGroups: logi TRUE)
RAM: 0.00MB
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] Biobase_2.6.0 aroma.affymetrix_1.3.0
aroma.apd_0.1.7 affxparser_1.18.0
[5] R.huge_0.2.0 aroma.core_1.3.1
aroma.light_1.15.1 matrixStats_0.1.8
[9] R.rsp_0.3.6 R.filesets_0.6.5
digest_0.4.1 R.cache_0.2.0
[13] R.utils_1.2.4 R.oo_1.6.5
affy_1.24.2 R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] affyio_1.14.0 preprocessCore_1.8.0
How can i get more details on the error.
I tried to use less CEL files and as few as 3, still no luck.
Thanks in advance
On Feb 24, 10:46 am, Henrik Bengtsson <henrik.bengts...@gmail.com>
wrote:
> 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
>
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
>
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> > athttp://groups.google.com/group/aroma-affymetrix?hl=en- Hide quoted text -
>
> - Show quoted text -
--
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