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

[emilie sohier]

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