[BioC] crlmm and cluster centres error
rvidal at gmail.com
Tue Sep 14 20:55:59 CEST 2010
As I get acquainted with R and Bioconductor, I've been trying to look at some SNP6 microarrays using crlmm and have been running in to many speed bumps.
I'm trying to look at two CEL files (samples) and considering it is a small number of samples, I assumed the bare basic example from the manual would be sufficient but I run into the following problem:
"Error: number of cluster centres must lie between 1 and nrow(x)"
Where would I define the cluster centres? Is this an issue with the CEL files?
Any help is well appreciated.
> path <- "input/dna/"
> celFiles <- list.celfiles(path, full.names=TRUE)
> system.time(clrmmResult <- crlmm(celFiles, verbose = FALSE))
Welcome togenomewidesnp6Crlmmversion 1.0.2
Error: number of cluster centres must lie between 1 and nrow(x)
Timing stopped at: 62.81 1.45 64.25
R version 2.11.1 (2010-05-31)
 LC_COLLATE=English_United States.1252
 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252
 LC_TIME=English_United States.1252
attached base packages:
 tools stats graphics grDevices utils datasets methods
other attached packages:
 genomewidesnp6Crlmm_1.0.2 hapmapsnp6_1.3.3
 ff_2.1-2 bit_1.1-4
 crlmm_1.6.5 oligoClasses_1.10.0
loaded via a namespace (and not attached):
 affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2
 Biostrings_2.16.9 DBI_0.2-5 ellipse_0.3-5
 genefilter_1.30.0 IRanges_1.6.17 mvtnorm_0.9-92
 preprocessCore_1.10.0 RSQLite_0.9-2 splines_2.11.1
 survival_2.35-8 xtable_1.5-6
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