Hello everyone, I am attempting to run the sample commands given in the CRLMM version 2 vignette. After loading the crlmm library and hapmapsnp6 library I have run the following commands: Jenna's R> path <- system.file("celFiles", package="hapmapsnp6") Jenna's R> celFiles <- list.celfiles(path, full.names=TRUE) Jenna's R> system.time(crlmmResult <- crlmm(celFiles, verbose=TRUE)) Loading required package: genomewidesnp6Crlmm Welcome togenomewidesnp6Crlmmversion 1.0.4 Loading annotations and mixture model parameters. Processing 3 files.  |==================================================| 100% Loading annotations. Determining gender. Calling 906600 SNPs for recalibration... Done. Estimating recalibration parameters. Calling 906600 SNPs... Done.   user  system elapsed 281.242   7.256 298.400 Warning message: In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]],  :  Recalibration not possible. Possible cause: small sample size. After I get this when I attempt to look at the results, using crlmmResult[["calls"]][1:10, ] I get NULL. There are no results anywhere in crlmmResults.  I have tried running this with both hapmapsnp5 and hapmapsnp6. Here is my session information: Jenna's R> sessionInfo() R version 2.12.1 (2010-12-16) Platform: i686-pc-linux-gnu (32-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 [6] methods   base other attached packages: [1] genomewidesnp6Crlmm_1.0.4 hapmapsnp6_1.3.3 [3] crlmm_1.8.11              oligo_1.14.0 [5] oligoClasses_1.12.2       Biobase_2.10.0 loaded via a namespace (and not attached):  [1] affxparser_1.22.1     affyio_1.18.0  [3] annotate_1.28.1       AnnotationDbi_1.12.1  [5] Biostrings_2.18.4     bit_1.1-7  [7] DBI_0.2-5             ellipse_0.3-5  [9] ff_2.2-3              genefilter_1.32.0 [11] IRanges_1.8.9         mvtnorm_0.9-95 [13] preprocessCore_1.12.0 RSQLite_0.9-4 [15] splines_2.12.1        survival_2.36-2 [17] tcltk_2.12.1          tools_2.12.1 [19] xtable_1.5-6 If anyone has come across this or can provide me with some guidance I would greatly appreciate it. Thank you in advance. Sincerely, Jenna Butler -- Jenna L Butler PhD Computer Science Candidate 2014 University of Western Ontario, Canada jcamer7@uwo.ca http://www.csd.uwo.ca/People/gradstudents/jcamer7/ [[alternative HTML version deleted]]

Hi Jenna, can you please point me to the vignette you're looking at? The proper way of accessing the genotype calls is: theCalls = calls(crlmmResult) Similarly, if you need access to the confidence scores: theConfsProb = confs(crlmmResult) ## probability scale theConfsIntg = confs(crlmmResult, FALSE) ## "integer" scale - uses less RAM benilton On 17 August 2011 16:56, Jenna Cameron <jcamer7 at="" uwo.ca=""> wrote: > Hello everyone, > > I am?attempting?to run the sample commands given in the CRLMM version 2 vignette. After loading the crlmm library and hapmapsnp6 library I have run the following commands: > > > > Jenna's R> path <- system.file("celFiles", package="hapmapsnp6") > Jenna's R> celFiles <- list.celfiles(path, full.names=TRUE) > Jenna's R> system.time(crlmmResult <- crlmm(celFiles, verbose=TRUE)) > Loading required package: genomewidesnp6Crlmm > Welcome togenomewidesnp6Crlmmversion 1.0.4 > Loading annotations and mixture model parameters. > Processing 3 files. > ??|==================================================| 100% > Loading annotations. > Determining gender. > Calling 906600 SNPs for recalibration... Done. > Estimating recalibration parameters. > Calling 906600 SNPs... Done. > ???user ?system elapsed > 281.242 ??7.256?298.400 > Warning message: > In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]], ?: > ??Recalibration not possible. Possible cause: small sample size. > > > > After I get this when I attempt to look at the results, using?crlmmResult[["calls"]][1:10, ] I get NULL. There are no results anywhere in crlmmResults. ?I have tried running this with both hapmapsnp5 and hapmapsnp6. > > > Here is my session information: > Jenna's R> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: i686-pc-linux-gnu (32-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 > [6] methods ? base > > > other attached packages: > [1] genomewidesnp6Crlmm_1.0.4 hapmapsnp6_1.3.3 > [3] crlmm_1.8.11 ? ? ? ? ? ? ?oligo_1.14.0 > [5] oligoClasses_1.12.2 ? ? ? Biobase_2.10.0 > > > loaded via a namespace (and not attached): > ?[1] affxparser_1.22.1 ? ? affyio_1.18.0 > ?[3] annotate_1.28.1 ? ? ? AnnotationDbi_1.12.1 > ?[5] Biostrings_2.18.4 ? ? bit_1.1-7 > ?[7] DBI_0.2-5 ? ? ? ? ? ? ellipse_0.3-5 > ?[9] ff_2.2-3 ? ? ? ? ? ? ?genefilter_1.32.0 > [11] IRanges_1.8.9 ? ? ? ? mvtnorm_0.9-95 > [13] preprocessCore_1.12.0 RSQLite_0.9-4 > [15] splines_2.12.1 ? ? ? ?survival_2.36-2 > [17] tcltk_2.12.1 ? ? ? ? ?tools_2.12.1 > [19] xtable_1.5-6 > > > > > If anyone has come across this or can provide me with some guidance I would greatly appreciate it. Thank you in advance. > > > Sincerely, > Jenna Butler > -- > Jenna L Butler > PhD Computer Science Candidate 2014 > University of Western Ontario, Canada > jcamer7 at uwo.ca > http://www.csd.uwo.ca/People/gradstudents/jcamer7/ > > ? ? ? ?[[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 > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)