Dear Benilton,
I tried the crlmm function,
but it returns a very similar error, as you can see below.
I hope that this will be useful.
Other suggestions?
Thanks for your help,
Alessio
> crlmm(fullFilenames,outDir)
Loading required package: pd.genomewidesnp.6
Normalization: 100.00 percent done.
Genotyping: 000.00 percent done.Error in
getGenotypeRegionParams(alleleA[index, ] - alleleB[index, ], :
INTEGER() can only be applied to a 'integer', not a 'NULL'
> traceback()
4: .Call("R_trimmed_stats", M + (initialcalls - 2) * f,
as.integer(initialcalls),
0.025)
3: getGenotypeRegionParams(alleleA[index, ] - alleleB[index, ],
initialCalls[index, ], fs[index, ], verbose = FALSE)
2: genotypeOne(filenames, outdir, batch_size = batch_size, balance =
balance,
minLLRforCalls = minLLRforCalls, recalibrate = recalibrate,
verbose = verbose, pkgname = pkgname, reference = reference)
1: crlmm(fullFilenames, outDir)
On Tue, 2009-02-10 at 12:13 -0200, Benilton Carvalho wrote:
> Alessio,
>
> thanks for your report. I've identified the problem and already have
a
> solution for it.
>
> In the meantime, you could use crlmm() instead:
>
> library(oligo)
> outDir = "tmp" ## this will be created by crlmm()
> fullFilenames = list.celfiles("/home/alessio/Documents/martinelli",
> full.names=TRUE)
> crlmm(fullFilenames, outDir)
>
> and, if you want the summaries:
>
> alleleA = readSummaries("alleleA", outDir)
> alleleB = readSummaries("alleleB", outDir)
>
> Let me know how it goes.
>
> b
>
> On Feb 10, 2009, at 11:58 AM, alessio boattini wrote:
>
> > Dear All,
> >
> > I am working with Affymetrix Genome Wide Human SNP Array 6.0 data.
> > While pre-processing the data with the justSNPRMA function
(library
> > "oligo"), I obtained the error described below.
> > An analogous problem was reported there:
> >
http://article.gmane.org/gmane.science.biology.informatics.conduct
or/17495
> > but there was no answer.
> > Any hint?
> > Many thanks
> > Alessio
> >
> >> library(oligo)
> > ...
> >> setwd("/home/alessio/Documents/martinelli")
> >> fullFilenames=list.celfiles()
> >> fullFilenames
> > [1] "20081009_1_SNP6.CEL"
> >> preProcData=justSNPRMA(fullFilenames)
> > Reading CEL files.
> > Normalizing to Hapmap.
> > Summarizing.
> > Error in justSNPRMA(fullFilenames) :
> > INTEGER() can only be applied to a 'integer', not a 'NULL'
> >
> >> traceback()
> > 2: .Call("rma_c_complete_copy", tmpExprs, tmpExprs, pnVec,
> > length(unique(pnVec)),
> > body(bg.dens), new.env(), FALSE, FALSE, as.integer(2),
PACKAGE =
> > "oligo")
> > 1: justSNPRMA(fullFilenames)
> >
> >> sessionInfo()
> > R version 2.8.1 (2008-12-22)
> > i686-pc-linux-gnu
> >
> > locale:
> > LC_CTYPE
> > =
> > en_GB
> > .UTF
> > -8
> > ;LC_NUMERIC
> > =
> > C
> > ;LC_TIME
> > =
> > en_GB
> > .UTF
> > -8
> > ;LC_COLLATE
> > =
> > en_GB
> > .UTF
> > -8
> > ;LC_MONETARY
> > =
> > C
> > ;LC_MESSAGES
> > =
> > en_GB
> > .UTF
> > -8
> > ;LC_PAPER
> > =
> > en_GB
> > .UTF
> > -8
> > ;LC_NAME
> > =
> > C
> > ;LC_ADDRESS
> > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] splines tools stats graphics grDevices utils
> > datasets
> > [8] methods base
> >
> > other attached packages:
> > [1] pd.genomewidesnp.6_0.4.2 oligo_1.6.0
> > oligoClasses_1.4.0
> > [4] affxparser_1.14.2 AnnotationDbi_1.4.2
> > preprocessCore_1.4.0
> > [7] RSQLite_0.7-1 DBI_0.2-4
> > Biobase_2.2.1
> > [10] vegan_1.15-1
> >
> > _______________________________________________
> > 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
>
