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

[Benilton Carvalho]

What's the result of:

summary(gensnp$SNR)

?

On 18 June 2010 13:44, emilie sohier <emilie.sohier15 at orange.fr> 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
>> >
>> > _______________________________________________
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>> >
>>
>>
>
>
>