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$SNR) > Min. 1st Qu. Median Mean 3rd Qu. Max. > 2.895 4.784 5.343 5.408 6.052 8.696 > > > > >> Message du 18/06/10 15:03 >> De : "Benilton Carvalho" >> A : "emilie sohier" >> Copie ? : "bioconductor" >> Objet : Re: [BioC] crlmm package help for copy number affymetrix snp 6.0 >> >> >> What's the result of: >> >> summary(gensnp$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 ? : "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="genomewide snp6",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 >> >> > >> >> >> >> >> > >> > >> > >> >> > > >