[BioC] crlmmCopyNumber and batch issues

Ricardo Vidal rvidal at gmail.com
Thu Nov 11 01:51:32 CET 2010


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.

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)

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) 

[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.


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