[BioC] Problem with justSNPRMA, library "oligo"

[alessio boattini]

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.conductor/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
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>