[BioC] Problem with justSNPRMA, library "oligo"

[Henrik Bengtsson]

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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