Hi Benilton Thanks again for your instruction. I set the gender=NULL, and the error still came up. If due to sample size, I will try add another 2 samples, total 4 samples to see if it work. Thanks. J. > system.time(crlmmResult <- crlmm(celFiles, gender=NULL, verbose = FALSE)) Welcome togenomewidesnp6Crlmmversion 1.0.4 Error: number of cluster centres must lie between 1 and nrow(x) Timing stopped at: 46.67 1.29 47.982 > ________________________________ From: Benilton Carvalho <beniltoncarvalho@gmail.com> Cc: "Bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Thursday, October 20, 2011 5:05 AM Subject: Re: Erros in crlmm Re: [BioC] SNP 6 chip Enter manually the gender of the samples through the "gender" argument. You'll also see a warning (not error) saying that it could not do recalibration and that's due to the small sample size. b Hi Benilton and all, > >Thanks for kind suggestions. I am eager to try crlmm with 2 samples, but error message "Error: number of cluster centres must lie between 1 and nrow(x)". Details were shown below. Any further suggestions will be appreciated. J. > >Error: number of cluster centres must lie between 1 and nrow(x) > >> celFiles >[1] "/tmp/data//00-0523B_SNP_6-0.CEL" "/tmp/data//02-0476B_SNP_6-0.CEL" >> crlmmResult <- crlmm(celFiles) > >crlmmResult <- crlmm(celFiles) >Loading annotations and mixture model parameters. >Processing 2 files. >  |================================================================== ====| 100% >Loading annotations. >Determining gender. >Error: number of cluster centres must lie between 1 and nrow(x) >> >> sessionInfo() > >sessionInfo() >R version 2.13.2 (2011-09-30) >Platform: x86_64-unknown-linux-gnu (64-bit) > >locale: > [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8       LC_NAME=C > [9] LC_ADDRESS=C               LC_TELEPHONE=C >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >attached base packages: >[1] stats     graphics  grDevices utils     datasets  methods   base > >other attached packages: >[1] genomewidesnp6Crlmm_1.0.4 crlmm_1.10.0 >[3] oligoClasses_1.14.0       Biobase_2.12.2 > >loaded via a namespace (and not attached): > [1] affyio_1.20.0         annotate_1.30.1       AnnotationDbi_1.14.1 > [4] Biostrings_2.20.4     bit_1.1-7             DBI_0.2-5 > [7] ellipse_0.3-5         ff_2.2-3              genefilter_1.34.0 >[10] IRanges_1.10.6        mvtnorm_0.9-9991 preprocessCore_1.14.0 >[13] RSQLite_0.10.0        splines_2.13.2        survival_2.36-9 >[16] xtable_1.6-0 >> >> > > > > >________________________________ > From: Benilton Carvalho <beniltoncarvalho@gmail.com> >To: cstrato <cstrato@aon.at> >Cc: James W. MacDonald <jmacdon@med.umich.edu>; "Bioconductor@r-project.org" <bioconductor@r-project.org> >Sent: Wednesday, October 19, 2011 5:25 PM >Subject: Re: [BioC] SNP 6 chip > >for 250K, you can genotype with the CRLMM algorithm in oligo. > >for SNP 6.0, use the crlmm package instead... the implementation >currently available there is an upgrade of the one in oligo, using >features exclusive for SNP 6.0... the crlmm package also offers a CN >tool (details on the vignette). > >b > >On 19 October 2011 22:12, cstrato <cstrato@aon.at> wrote: >> Dear Jim, >> >> Thank you for mentioning xps, however xps does only work for expression >> arrays and not for mapping arrays such as SNP6. >> >> Best regards >> Christian >> >> >> On 10/19/11 10:51 PM, James W. MacDonald wrote: >>> >>> Hi John, >>> >>> On 10/19/2011 2:27 PM, John linux-user wrote: >>>> >>>> Hello, >>>> >>>> Can you please suggest R packages for analyzing affy SNP 6 and 250K as >>>> well as copy number variations for sequencing data? Thanks. >>> >>> The oligo package will do this (although I don't know if it can do the >>> CNV part). You might also look at xps. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> John >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > >-- >Successful people ask better questions, and as a result, they get >better answers. (Tony Robbins) > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]