[BioC] oligo: error in crlmm function

[Benilton Carvalho]

Hi Javier,

I'll take a look at this... But, in the meantime, I'd strongly
recommend you to use the crlmm package for SNP 5 and SNP6 (or
Illumina) chips. The reason is that the algorithm implemented there is
an upgrade on the one in oligo and provides more precise and accurate
calls.

benilton

On 4 June 2012 09:58, Javier Pérez Florido <jpflorido at gmail.com> wrote:
> Dear list,
> I'm trying to obtain genotype calls from genome wide SNP arrays  (affymetrix
> 6.0) using oligo package, but the following error comes up:
>
> library(oligo)
> fullFilenames<-list.celfiles(full.names=TRUE)
> fullFilenames
> [1] "./E10897_(GenomeWideSNP_6)_2.CEL" "./E10905_(GenomeWideSNP_6).CEL"
> [3] "./E10906_(GenomeWideSNP_6).CEL"   "./E10915_(GenomeWideSNP_6).CEL"
> [5] "./E10916_(GenomeWideSNP_6).CEL"
> outputDir<-file.path(getwd(),"crlmmResults")
>
> crlmm(fullFilenames,outputDir)
> Loading required package: pd.genomewidesnp.6
> Loading required package: RSQLite
> Loading required package: DBI
> Loading results from previous normalization/summarization step.
> Error in readChar(con, 5L, useBytes = TRUE) :
>  cannot open connection
> Además: Mensajes de aviso perdidos
> In readChar(con, 5L, useBytes = TRUE) :
>  cannot open compressed file
> '/media/data/ArraysSNPs/PTC/prueba/crlmmResults/NormalizationSummarizationOutput.rda',
> probable reason 'No such file or directory'
>
> The output directory exists and has correct permissions.
> Any tips?
> Thanks in advance,
> Javier
>
>
>
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=es_ES.UTF-8
>  [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pd.genomewidesnp.6_1.2.2 RSQLite_0.11.1           DBI_0.2-5
> [4] oligo_1.16.2             preprocessCore_1.14.0    oligoClasses_1.14.0
> [7] Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.24.0 affyio_1.20.0     Biostrings_2.20.4 bit_1.1-8
> [5] ff_2.2-7          IRanges_1.10.6    splines_2.13.1
>
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