Ok, before we try to troubleshoot this one, please update to the
latest aroma.affymetrix version. The one you are using is nearly
three months old, and I prefer to troubleshoot the current code base.
When you've done that, it should be enough to run plotRle(); you don't
have to rerun everything.
BTW, did you remember to call fit() on the probe-level model?
/Henrik
On Wed, Feb 24, 2010 at 8:15 PM, zaid <z...@genomedx.com> wrote:
>>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 -
>
> --
> 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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--
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version of the package, 2) to report the output of sessionInfo() and
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