Erros in crlmm Re: SNP 6 chip
0
0
Entering edit mode
@benilton-carvalho-1375
Last seen 18 months ago
Brazil/Campinas/UNICAMP
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)
SNP Sequencing affy oligo xps crlmm SNP Sequencing affy oligo xps crlmm • 520 views
ADD COMMENT

Login before adding your answer.

Traffic: 342 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6