Dear list, I'm trying to obtain genotype calls from genome wide SNP arrays (affymetrix 6.0) using oligo package, but the following error comes up: library(oligo) fullFilenames<-list.celfiles(full.names=TRUE) fullFilenames [1] "./E10897_(GenomeWideSNP_6)_2.CEL" "./E10905_(GenomeWideSNP_6).CEL" [3] "./E10906_(GenomeWideSNP_6).CEL" "./E10915_(GenomeWideSNP_6).CEL" [5] "./E10916_(GenomeWideSNP_6).CEL" outputDir<-file.path(getwd(),"crlmmResults") crlmm(fullFilenames,outputDir) Loading required package: pd.genomewidesnp.6 Loading required package: RSQLite Loading required package: DBI Loading results from previous normalization/summarization step. Error in readChar(con, 5L, useBytes = TRUE) : cannot open connection Adem?s: Mensajes de aviso perdidos In readChar(con, 5L, useBytes = TRUE) : cannot open compressed file '/media/data/ArraysSNPs/PTC/prueba/crlmmResults/NormalizationSummariza tionOutput.rda', probable reason 'No such file or directory' The output directory exists and has correct permissions. Any tips? Thanks in advance, Javier > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=es_ES.UTF-8 [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.genomewidesnp.6_1.2.2 RSQLite_0.11.1 DBI_0.2-5 [4] oligo_1.16.2 preprocessCore_1.14.0 oligoClasses_1.14.0 [7] Biobase_2.12.2 loaded via a namespace (and not attached): [1] affxparser_1.24.0 affyio_1.20.0 Biostrings_2.20.4 bit_1.1-8 [5] ff_2.2-7 IRanges_1.10.6 splines_2.13.1

Hi Javier, I'll take a look at this... But, in the meantime, I'd strongly recommend you to use the crlmm package for SNP 5 and SNP6 (or Illumina) chips. The reason is that the algorithm implemented there is an upgrade on the one in oligo and provides more precise and accurate calls. benilton On 4 June 2012 09:58, Javier P?rez Florido <jpflorido at="" gmail.com=""> wrote: > Dear list, > I'm trying to obtain genotype calls from genome wide SNP arrays ?(affymetrix > 6.0) using oligo package, but the following error comes up: > > library(oligo) > fullFilenames<-list.celfiles(full.names=TRUE) > fullFilenames > [1] "./E10897_(GenomeWideSNP_6)_2.CEL" "./E10905_(GenomeWideSNP_6).CEL" > [3] "./E10906_(GenomeWideSNP_6).CEL" ? "./E10915_(GenomeWideSNP_6).CEL" > [5] "./E10916_(GenomeWideSNP_6).CEL" > outputDir<-file.path(getwd(),"crlmmResults") > > crlmm(fullFilenames,outputDir) > Loading required package: pd.genomewidesnp.6 > Loading required package: RSQLite > Loading required package: DBI > Loading results from previous normalization/summarization step. > Error in readChar(con, 5L, useBytes = TRUE) : > ?cannot open connection > Adem?s: Mensajes de aviso perdidos > In readChar(con, 5L, useBytes = TRUE) : > ?cannot open compressed file > '/media/data/ArraysSNPs/PTC/prueba/crlmmResults/NormalizationSummari zationOutput.rda', > probable reason 'No such file or directory' > > The output directory exists and has correct permissions. > Any tips? > Thanks in advance, > Javier > > > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > ?[1] LC_CTYPE=es_ES.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=es_ES.UTF-8 ? ? ? ?LC_COLLATE=es_ES.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=es_ES.UTF-8 > ?[7] LC_PAPER=es_ES.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] pd.genomewidesnp.6_1.2.2 RSQLite_0.11.1 ? ? ? ? ? DBI_0.2-5 > [4] oligo_1.16.2 ? ? ? ? ? ? preprocessCore_1.14.0 ? ?oligoClasses_1.14.0 > [7] Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.24.0 affyio_1.20.0 ? ? Biostrings_2.20.4 bit_1.1-8 > [5] ff_2.2-7 ? ? ? ? ?IRanges_1.10.6 ? ?splines_2.13.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor