sorry, please note the typo on my previous email. corrected version below: if females, use: crlmm(celFiles, gender=c(2, 2)) b On 20 October 2011 12:41, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > that not what i meant. > > if males, you should run: > > crlmm(celFiles, gender=c(1, 1)) > > if females: > > crlmm(celFiles, gender=c(1, 2)) > > or the combination of the above that holds for your dataset. > > b > > On 20 October 2011 12:19, John linux-user <johnlinuxuser at="" yahoo.com=""> wrote: >> 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 at="" gmail.com=""> >> To: John linux-user <johnlinuxuser at="" yahoo.com=""> >> Cc: "Bioconductor at r-project.org" <bioconductor at="" 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 >> On Oct 20, 2011 2:45 AM, "John linux-user" <johnlinuxuser at="" yahoo.com=""> wrote: >> >> 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 at="" gmail.com=""> >> To: cstrato <cstrato at="" aon.at=""> >> Cc: James W. MacDonald <jmacdon at="" med.umich.edu="">; "Bioconductor at r-project.org" >> <bioconductor at="" 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 at="" 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 at 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 at 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 at 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) > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)