Updated all my packages:
> 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)
>> 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] affyQCReport_1.24.0 lattice_0.17-26
RColorBrewer_1.0-2 preprocessCore_1.8.0
[5] xtable_1.5-6 simpleaffy_2.22.0
gcrma_2.18.0 genefilter_1.28.1
[9] Biobase_2.6.0 aroma.affymetrix_1.4.0
aroma.apd_0.1.7 affxparser_1.18.0
[13] R.huge_0.2.0 aroma.core_1.4.0
aroma.light_1.15.1 matrixStats_0.1.9
[17] R.rsp_0.3.6 R.filesets_0.7.0
digest_0.4.2 R.cache_0.2.0
[21] R.utils_1.3.3 R.oo_1.6.7
affyPLM_1.22.0 affy_1.24.2
[25] R.methodsS3_1.1.0
loaded via a namespace (and not attached):
[1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1
Biostrings_2.14.8
[5] DBI_0.2-5 grid_2.10.0 IRanges_1.4.8
RSQLite_0.8-3
[9] splines_2.10.0 survival_2.35-7 tools_2.10.0
> plotNuse(qamTr)
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
$yaxs) :
NAs not allowed in 'ylim'
> plotRle(qamTr)
Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars
$yaxs) :
NAs not allowed in 'ylim'
> cesTr <- getChipEffectSet(plmTr)
> trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
> head(trFit)
unitName groupName unit group cell S370-A-HuEx-1_0-st-v2-01-1
(S09-13138)
1 2315251 2315252 1 1
1 0
2 2315373 2315374 2 1
3 0
3 2315554 2315586 3 1
7 0
S371-A-HuEx-1_0-st-v2-01-1 (S09-07848)
1 0
2 0
3 0
Yes I have done fit() call using : fit(plmTr, verbose=verbose)
Mark,
I have tried 53 samples, 3 of the 53, 12 of the 53.
A different set of CEL files of 13, 10 and 3.
As well as different binary CDF files.
I have created folders from scratch still no luck on HuEx, however
u95A, and plus2 works with no problems.
Thanks again for all the help.
Would you like more information?
Thanks in advance
Zaid
On Feb 24, 2:10 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote:
> Hi Zaid.
>
> Another thing to check/report in your next update (after you update to
> the new aroma.affymetrix) is whether you have reasonable chip
> effects. This is what Henrik was eluding to in his last comment.
> bxp() which is eventually called by plotRle() will handle NAs, so that
> shouldn't be the problem. The thing it won't handle is if *all*
> values are NA or all equal to the same number e.g. 0. I seem to
> recall you had this issue before. For example, what does these
> commands give:
>
> [...all your previous stuff...]
> cesTr <- getChipEffectSet(plmTr)
> trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
>
> head(trFit)
>
> One thing that worries/interests me is your comment "I tried to use
> less CEL files and as few as 3". I've run plotRle() on 10s of samples
> and I suspect that is not the problem. Can you explain exactly what
> you tried?
>
> And, if not too much work, it may even be best to create a completely
> new directory as if you were starting from scratch (say, with a
> handful of files), run your entire script and report back.
>
> Cheers,
> Mark
>
> On 25-Feb-10, at 8:19 AM, Henrik Bengtsson wrote:
>
>
>
>
>
> > 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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> >>>> 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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>
> > --
> > 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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>
> ------------------------------
> Mark Robinson, PhD (Melb)
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robin...@garvan.org.au
> e: mrobin...@wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
> ------------------------------
>
> ______________________________________________________________________
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--
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traceback(), and 3) to post a complete code example.
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