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

[Benilton Carvalho]

after off-list communication with Emilie, the proposed solution is for
her to appropriately set the 'batch' argument on the genotype() call.

b

On 18 June 2010 14:08, emilie sohier <emilie.sohier15 at orange.fr> wrote:
> 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
>> >> >
>> >>
>> >>
>> >
>> >
>> >
>>
>>
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