Hi Zaid.
So, its looks like your boxplot problem is easily explainable. ALL of
your chip effects are 0. That'll lead to a fairly uninteresting RLE or
NUSE plot. Let's try and figure out why.
I assume you've done something like:
[...]
plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
fit(plmTr, verbose=verbose)
A couple things to check are:
1. Does your AffymetrixCelSet object 'csN' have reasonable data? Try ...
readUnits(csN, units=1:2)
2. If that looks fine, how about we re-fit the probe level models, just in
case it got interrupted for whatever reason. Try ...
fit(plmTr, verbose=verbose, force=TRUE)
... and then check whether the chip effects are non-zero, as before ...
cesTr <- getChipEffectSet(plmTr)
trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
head(trFit)
Report back on that when you get a chance.
Also, you said:
> 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.
But you didn't tell us exactly what you've done. Did you use separate
directories or did you use extract()?
Is there anything else that you saw while the data was processing that is
worth mentioning? Any strange errors/warnings? Did you accurately create
a custom CDF?
Cheers,
Mark
> 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.
>>
>> >>>> You received this message because you are subscribed to the
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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.
>>
>> > You received this message because you are subscribed to the Google
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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
>> ------------------------------
>>
>> ______________________________________________________________________
>> The information in this email is confidential and intended solely for
>> the addressee.
>> You must not disclose, forward, print or use it without the permission
>> of the sender.
>> ______________________________________________________________________-
>> 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.
>
>
> You received this message because you are subscribed to the Google Groups
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>
______________________________________________________________________
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