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

[emilie sohier]

The result is :

> summary(gensnp$SNR)
Min. 1st Qu. Median Mean 3rd Qu. Max. 
2.895 4.784 5.343 5.408 6.052 8.696 




> Message du 18/06/10 15:03
> De : "Benilton Carvalho" 
> A : "emilie sohier" 
> Copie à : "bioconductor" 
> Objet : Re: [BioC] crlmm package help for copy number affymetrix snp 6.0
> 
> 
> What's the result of:
> 
> summary(gensnp$SNR)
> 
> ?
> 
> On 18 June 2010 13:44, emilie sohier  wrote:
> >
> > 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
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor at stat.math.ethz.ch
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >>
> >>
> >
> >
> >
> 
>