Question: Reading Affy CEL files
4.9 years ago by
Guest User • 12k
Guest User • 12k wrote:
I am a newbie to Affy. Thanks for your help. I am processing CEL files through R (Affy package) and am having some basic issues that I am not finding satisfactory answers to (have googled). The chip used is hugene11stv1. I also am using the hugene11stprobeset.db to try to do probeset ???> Symbol translation. Essentially, I want to create a file with gene expression data, with genes * samples as my final matrix. Code: setwd(wDir); Data <- ReadAffy(); eset <- rma(Data); write.exprs(eset,file="geneExpData.txt", sep="\t", quote = F); When I analyze the file written, I see that the number of columns is as I expect(number samples) but there are 33,297 genes. Please help me understand a few fundamental aspects here: 1. I tried translating these Affy IDs to gene symbols to see if that would make my analysis easier. Here are some things I tried Try 1: symbols <- getSYMBOL(as.character(expr.matrix[,1]), "hugene11stprobeset"); ???> Not quite working. Only ~175 of the probeset IDs are getting translated. Try 2: symbs <- mget(featureNames(eset), hugene11stprobesetSYMBOL, ifnotfound =NA); symbs <- unlist(symbs) mat <- eset; # make a copy featureNames(mat) <- ifelse(!is.na(symbs), symbs, featureNames(mat)) Many NAs. Can you please help me understand what is happening here. -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  hugene11stv1cdf_2.3.0 affy_1.36.1 Biobase_2.18.0  BiocGenerics_0.4.0 loaded via a namespace (and not attached):  affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0  tools_2.15.3 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
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