Hi, I'm trying to perform some analysis on SNP6 arrays (Affymetrix) and am running into some issues when attempting to perform the crlmmCopyNumber step in my R code. I've set up a Phenotype file where I list my files and their Batch groups. In my example case, group1 and group2 Name FileName Batch A1 array-123.CEL group1 A2 array-223.CEL group1 A3 array.214.CEL group2 And so on for roughly 24 arrays. 11 in group1, 13 in group2. setwd("../Projects/dna/") library(affy) library(crlmm) cdfName <- "genomewidesnp6" celPath <- "input" outDir <- "output" celFiles <- list.celfiles(celPath, full.names=TRUE) myPhenoFile <- "gr1-gr2-pheno.txt" pd <- read.AnnotatedDataFrame(myPhenoFile, header=TRUE, row.names=1, as.is=TRUE) batch <- as.factor(pd$Batch) gensnp <- genotype(celFiles, cdfName=cdfName, copynumber=TRUE, batch=batch) cnSet=crlmmCopynumber(gensnp) This last step then takes a while to go through all the chromosomes and halts at chromosome 17 with the following error: ... Chromosome 15 Batch 1 of 2 Batch 2 of 2 Chromosome 16 Batch 1 of 2 Batch 2 of 2 Chromosome 17 Batch 1 of 2 Error in oneBatch(object, cnOptions = cnOptions, tmp.objects = tmp.objects) : fewer than 200 snps pass criteria for predicting the sufficient statistics ----- I'm not sure what I may be missing here. If I don't define the batch this doesn't at all. Now with my batches it seems to work up to Chromosome 17. My session info: > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] genomewidesnp6Crlmm_1.0.2 crlmm_1.6.5 oligoClasses_1.10.0 [4] affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 Biostrings_2.16.9 [5] bit_1.1-4 DBI_0.2-5 ellipse_0.3-5 ff_2.1-2.1 [9] genefilter_1.30.0 IRanges_1.6.17 mvtnorm_0.9-92 preprocessCore_1.10.0 [13] RSQLite_0.9-2 splines_2.11.1 survival_2.35-8 tools_2.11.1 [17] xtable_1.5-6 Any help is much appreciated. Kindly, Ricardo

For future reference, as suggested by Benilton Carvalho, I needed to use the latest version of R and crlmm. All working correctly now. Ricardo On 2010-11-10, at 7:51 PM, Ricardo Vidal wrote: > Hi, > > I'm trying to perform some analysis on SNP6 arrays (Affymetrix) and am running into some issues when attempting to perform the crlmmCopyNumber step in my R code. > > I've set up a Phenotype file where I list my files and their Batch groups. In my example case, group1 and group2 > Name FileName Batch > A1 array-123.CEL group1 > A2 array-223.CEL group1 > A3 array.214.CEL group2 > > And so on for roughly 24 arrays. 11 in group1, 13 in group2. > > setwd("../Projects/dna/") > library(affy) > library(crlmm) > cdfName <- "genomewidesnp6" > celPath <- "input" > outDir <- "output" > celFiles <- list.celfiles(celPath, full.names=TRUE) > myPhenoFile <- "gr1-gr2-pheno.txt" > pd <- read.AnnotatedDataFrame(myPhenoFile, header=TRUE, row.names=1, as.is=TRUE) > batch <- as.factor(pd$Batch) > gensnp <- genotype(celFiles, cdfName=cdfName, copynumber=TRUE, batch=batch) > cnSet=crlmmCopynumber(gensnp) > > This last step then takes a while to go through all the chromosomes and halts at chromosome 17 with the following error: > ... > Chromosome 15 > Batch 1 of 2 > Batch 2 of 2 > Chromosome 16 > Batch 1 of 2 > Batch 2 of 2 > Chromosome 17 > Batch 1 of 2 > Error in oneBatch(object, cnOptions = cnOptions, tmp.objects = tmp.objects) : > fewer than 200 snps pass criteria for predicting the sufficient statistics > > ----- > > I'm not sure what I may be missing here. If I don't define the batch this doesn't at all. Now with my batches it seems to work up to Chromosome 17. > > My session info: >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] genomewidesnp6Crlmm_1.0.2 crlmm_1.6.5 oligoClasses_1.10.0 > [4] affy_1.26.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2 Biostrings_2.16.9 > [5] bit_1.1-4 DBI_0.2-5 ellipse_0.3-5 ff_2.1-2.1 > [9] genefilter_1.30.0 IRanges_1.6.17 mvtnorm_0.9-92 preprocessCore_1.10.0 > [13] RSQLite_0.9-2 splines_2.11.1 survival_2.35-8 tools_2.11.1 > [17] xtable_1.5-6 > > > Any help is much appreciated. > > Kindly, > Ricardo >