[BioC] crlmm and cluster centres error

Ricardo Vidal rvidal at gmail.com
Tue Sep 14 21:48:37 CEST 2010


With the sample data it seems to work here too. However, with my 2 CEL files, not so much.

I've only managed to get anywhere with my CEL files if I play around with other parameters like setting gender=FALSE and setting batch=c("resistant", "sensitive") which doesn't make sense to me but works as a vector with the same length as the sample size (ie. length(celFiles) ).

Just following the example, it doesn't seem to work. I tried genotype this time round and only with the changes I mentioned above did I manage to get anywhere...

I'll try with other CEL files and see if I get different results.


Thanks,
Ricardo

On 2010-09-14, at 3:41 PM, Benilton Carvalho wrote:

> Hi Ricardo,
> 
> using the sample dataset in 'hapmapsnp6' works just fine for me. This
> is a tiny set with 3 samples. Even if I try it with 1 sample, the
> software behaves as expected...
> 
> It is possible this is an issue with the CEL files...
> 
> b
> 
>> system.time(clrmmResult <- crlmm(celFiles[1], verbose = FALSE))
>   user  system elapsed
> 88.439   1.300  89.744
> Warning message:
> In crlmmGT(res[["A"]], res[["B"]], res[["SNR"]], res[["mixtureParams"]],  :
>  Recalibration not possible. Possible cause: small sample size.
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
> 
> other attached packages:
> [1] genomewidesnp6Crlmm_1.0.2 hapmapsnp6_1.3.3
> [3] crlmm_1.6.5               oligoClasses_1.10.0
> [5] 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     bit_1.1-4             DBI_0.2-5
> [7] ellipse_0.3-5         ff_2.1-2              genefilter_1.30.0
> [10] 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
> [16] tools_2.11.1          xtable_1.5-6
>> 
> 
> 
> On 14 September 2010 19:55, Ricardo Vidal <rvidal at gmail.com> wrote:
>> Hi,
>> 
>> 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.
>> 
>> Best,
>> Ricardo
>> 
>> 
>>> 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)
>> i386-pc-mingw32
>> 
>> locale:
>> [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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