[BioC] crlmm and cluster centres error

Ricardo Vidal 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.


> library(crlmm)
> path <- "input/dna/"
> require(oligoClasses)
> library(hapmapsnp6)
> 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 

> sessionInfo()
R version 2.11.1 (2010-05-31) 

[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] genomewidesnp6Crlmm_1.0.2 hapmapsnp6_1.3.3         
[3] ff_2.1-2                  bit_1.1-4                
[5] crlmm_1.6.5               oligoClasses_1.10.0      
[7] Biobase_2.8.0            

loaded via a namespace (and not attached):
 [1] affyio_1.16.0         annotate_1.26.1       AnnotationDbi_1.10.2 
 [4] Biostrings_2.16.9     DBI_0.2-5             ellipse_0.3-5        
 [7] genefilter_1.30.0     IRanges_1.6.17        mvtnorm_0.9-92       
[10] preprocessCore_1.10.0 RSQLite_0.9-2         splines_2.11.1       
[13] survival_2.35-8       xtable_1.5-6         

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