[BioC] Problem with justSNPRMA, library "oligo"

[alessio boattini]

... hem ... that's it!

Thanks a lot!

Alessio

On Tue, 2009-02-10 at 07:43 -0800, Henrik Bengtsson wrote:
> Hi,
> 
> the SNPRMA preprocessing method requires two or more arrays.  This is
> because the probe summarization is done using the (two-way RMA-style)
> log-additive model.
> 
> /Henrik
> 
> Benilton, would you mind adding a test asserting that at least two
> arrays are passed, otherwise giving an error?
> 
> 
> On Tue, Feb 10, 2009 at 5:58 AM, alessio boattini
> <alessio.boattini2 at unibo.it> 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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> >