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

[emilie sohier]

I'have 95 samples.

Emilie

> Message du 18/06/10 14:37
> De : "Benilton Carvalho" 
> A : "emilie sohier" 
> Copie à : "bioconductor" 
> Objet : Re: [BioC] crlmm package help for copy number affymetrix snp 6.0
> 
> 
> 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  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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> 
>