[BioC] crlmm and HumanAffy250K SNP

[Benilton Carvalho]

Hi Nolwenn,

When it comes to Affymetrix arrays, the 'crlmm' package is exclusive
for SNP 5.0 and SNP 6.0 chips.

You can use the oligo package instead, which has the first
implementation of the crlmm algorithm that can be used with the 250K
arrays.

best,
b

On Mon, Apr 19, 2010 at 10:13 PM, Nolwenn Le Meur <nlemeur at irisa.fr> wrote:
> Hi everyone,
>
> I have just started exploring SNP data (GWA with pooled samples) and I
> am not sure I am using the right tools. I have Affy and Illumina data.
>
> For the Affy, I am trying to analyze HumanAffy250K SNP array using the
> crlmm package.
> First thing first, is it feasable ?
>
> I get the following message:
>
> library(crlmm)
> path <- c("~/project/gwa/affy/Affy/moins60-1")
> tempdir <- c("~/project/gwa/affy/Affy/tmp")
> celFiles <- list.celfiles(path, full.names=TRUE)
>
> crlmResult <- crlmm(celFiles[1:2])
>
> Loading required package: mapping250knspCrlmm
> If mapping250knspCrlmm is installed on an alternative location,
> pleaseload it manually by using library(mapping250knspCrlmm,lib.loc='/
> Altern/Lib/Loc')
> Error in snprma(filenames, fitMixture = TRUE, mixtureSampleSize =
> mixtureSampleSize,  :
>  Package mapping250knspCrlmm could not be found.
> In addition: Warning message:
> In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE,  :
>  there is no package called 'mapping250knspCrlmm'
>
> where can I find this package. I tried to download using the biocLite
> script but it does not exit.
>
> Should I use an other package?
>
>
> Any help is appreciated.
> Nolwenn
>
> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-04-09 r51652)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] crlmm_1.5.50        oligoClasses_1.9.57 Biobase_2.7.5
>
> loaded via a namespace (and not attached):
> [1] affyio_1.15.2        annotate_1.25.1      AnnotationDbi_1.9.8
> [4] Biostrings_2.15.27   bit_1.1-4            DBI_0.2-5
> [7] ellipse_0.3-5        ff_2.1-2             genefilter_1.29.6
> [10] IRanges_1.5.75       mvtnorm_0.9-9        preprocessCore_1.9.0
> [13] RSQLite_0.8-4        splines_2.12.0       survival_2.35-8
> [16] tools_2.12.0         xtable_1.5-6
>
>
>
>
> ------------------
> Nolwenn Le Meur
> IRISA Symbiose D151
> Université de Rennes I
> Campus Beaulieu
> 35042 Rennes Cedex
> France
> Phone: +33 2 99 84 71 17
> Fax: +33 2 99 84 71 71
> E-mail: nlemeur at irisa.fr
> Web: http://www.irisa.fr/symbiose/nolwenn_le_meur
>
>
>
>
>
>
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