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@irisa.fr
Web: http://www.irisa.fr/symbiose/nolwenn_le_meur






	[[alternative HTML version deleted]]

