[BioC] crlmmCopyNumber and batch issues

[Ricardo Vidal]

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
>