[BioC] GCRMA Error
Hooiveld, Guido
Guido.Hooiveld at wur.nl
Tue Nov 17 17:04:16 CET 2009
I am often using the combination of GCRMA and the remapped CDFs from the
Brainarray group for various arrays, and never got a problem...
So I downloaded the first three cel files from GSE9171 (GSM231709.CEL,
GSM231712.CEL, GSM231715.CEL), ran GCRMA, and indeed everything goes
fine.
Please note that I use a different name for the CDF than you do; I don't
know whether this may cause your problem? In my case the CDF and probe
file are automatically downloaded from the BioC repository.
HTH,
Guido
> library(affy)
> library(gcrma)
>
> affy.data <- ReadAffy(cdfname="hgu133plus2hsentrezg")
>
> x.norm <- gcrma(affy.data)
Adjusting for optical effect......Done.
Computing affinitiesLoading required package: AnnotationDbi .Done.
Adjusting for non-specific binding......Done.
Normalizing
Calculating Expression
>
> affy.data
AffyBatch object
size of arrays=1164x1164 features (8 kb) cdf=hgu133plus2hsentrezg (17788
affyids) number of samples=6 number of genes=17788
annotation=hgu133plus2hsentrezg notes=
> x.norm
ExpressionSet (storageMode: lockedEnvironment)
assayData: 17788 features, 3 samples
element names: exprs
phenoData
sampleNames: GSM231709.CEL, GSM231712.CEL, GSM231715.CEL (3 total)
varLabels and varMetadata description:
sample: arbitrary numbering
featureData
featureNames: 1_at, 10_at, ..., AFFX-TrpnX-M_at (17788 total)
fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation: hgu133plus2hsentrezg
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1
[3] hgu133plus2hsentrezgcdf_12.0.0 gcrma_2.16.0
[5] Biostrings_2.12.9 IRanges_1.2.3
[7] affy_1.22.1 Biobase_2.4.1
loaded via a namespace (and not attached):
[1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0
[4] RSQLite_0.7-1 splines_2.9.0 tools_2.9.0
>
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
internet: http://nutrigene.4t.com
email: guido.hooiveld at wur.nl
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhijin Wu
> Sent: 17 November 2009 05:58
> To: Denise Mauldin
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] GCRMA Error
>
> Hi Denise
>
> I'll download the dataset and try to reproduce the error
> first and get back to you
>
> Jean
>
> Denise Mauldin wrote:
> > Greetings all,
> >
> > I'm running gcrma on arrays from GSE9171 and I'm getting
> the infamous
> > 'NAs are not allowed in subscripted assignments' error.
> >
> >
> >> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570)
> >>
> > Adjusting for optical effect..............................Done.
> > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
> > NAs are not allowed in subscripted assignments
> >
> >> traceback()
> >>
> > 3: compute.affinities(cdfName(object), verbose = verbose)
> > 2: bg.adjust.gcrma(object, affinity.info = affinity.info,
> > affinity.source = affinity.source,
> > NCprobe = NCprobe, type = type, k = k, stretch = stretch,
> > correction = correction, GSB.adjust = GSB.adjust, rho = rho,
> > optical.correct = optical.correct, verbose = verbose, fast =
> > fast)
> > 1: gcrma(GSE9171_GPL570)
> >
> >> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE)
> >>
> > Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
> > NAs are not allowed in subscripted assignments
> >
> > Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray?
> > Is there something I can do to fix this?
> >
> > Thanks,
> > Denise
> >
> >
> >> sessionInfo()
> >>
> > R version 2.9.1 (2009-06-26)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
> >
> .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N
> >
> AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
> > FICATION=C
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1
> > [3] hgu133plus2hsentrezgcdf_11.0.1 gcrma_2.16.0
> > [5] Biostrings_2.12.10 IRanges_1.2.3
> > [7] limma_2.18.3 affy_1.22.1
> > [9] Biobase_2.4.1
> >
> > loaded via a namespace (and not attached):
> > [1] affyio_1.12.0 DBI_0.2-4 preprocessCore_1.6.0
> > [4] RSQLite_0.7-3 splines_2.9.1 tools_2.9.1
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
> --
> -------------------------------------------
> Zhijin (Jean) Wu
> Assistant Professor of Biostatistics
> Brown University, Box G-S121
> Providence, RI 02912
>
> Tel: 401 863 1230
> Fax: 401 863 9182
> http://www.stat.brown.edu/zwu
>
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