[BioC] crlmm package help for copy number affymetrix snp 6.0

[Benilton Carvalho]

Dear Emilie,

please check the documentation of crlmmCopynumber and note the
MIN.SAMPLES argument.

How many samples do you currently have?

b

On 18 June 2010 13:20, emilie sohier <emilie.sohier15 at orange.fr> wrote:
> Hello, i am a French bioinformatics student.
>
> I want to use the crlmm package to make the copy number of Genome-Wide Human SNP Array 6.0 Affymetrix
> but when i execute functions :
>
> gensnp=genotype(file.path("SNP6",filessnp),cdfName="genomewidesnp6",copynumber=TRUE)
> cnSet=crlmmCopynumber(gensnp)
> cn=copyNumber(cnSet)
>
>
> But i have the result
> cn
> .....
> SNP_A-1989634 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> SNP_A-1989647 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> SNP_A-1989659 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> SNP_A-4266322 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> SNP_A-1989663 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> SNP_A-1989664 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> .....
>
>
>
> And for the genotype i haven't any problems.
>
> Mi session Info:
>
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] crlmm_1.6.2 oligoClasses_1.10.0 Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.10.1 Biostrings_2.16.4 DBI_0.2-5
> [4] IRanges_1.6.6 RSQLite_0.9-1 affyio_1.16.0
> [7] annotate_1.26.0 bit_1.1-4 ellipse_0.3-5
> [10] ff_2.1-2 genefilter_1.30.0 mvtnorm_0.9-9
> [13] preprocessCore_1.10.0 splines_2.11.1 survival_2.35-8
> [16] tools_2.11.1 xtable_1.5-6
> Warning messages:
> 1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
> 2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>
>
> Thanks for your help.
> Emilie
>
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