[BioC] crlmm and cluster centres error

[Benilton Carvalho]

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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