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]]

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 > Universit? 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 > > > > > > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >