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anupam sinha ▴ 270
@anupam-sinha-3207
Last seen 8.2 years ago
Dear list, I use the following code to process some cel files I have : > dat<-ReadAffy() > dat_norm<-rma(dat) Background correcting Normalizing Calculating Expression > dat_norm_mat<-exprs(dat_norm) > write.table(dat_norm_mat,"GSE3185.txt",sep="\t",row.names=T,col.names= T,quote=F) and I get the following output in the text file : GSM48598.CEL GSM48599.CEL GSM48600.CEL GSM48601.CEL GSM48602.CEL 100_g_at 3.47028618802937 3.49106274273872 3.46940719815954 3.46836687956259 3.45079245249753 . . . I have couple of questions. 1) How do I add one more column to the text file which will give the gene symbol for each of the probe-id ? 2) Do the expression values get log2 transformed (after "rma" normalization is done on the cel files or I have to perform it separately) ? This is my sessionInfo(): R version 2.10.0 (2009-10-26) i386-redhat-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] splines tcltk stats graphics grDevices datasets utils [8] methods base other attached packages: [1] WGCNA_0.89 Hmisc_3.8-0 survival_2.35-7 [4] qvalue_1.22.0 flashClust_1.00 dynamicTreeCut_1.21 [7] impute_1.22.0 hgu95av2cdf_2.5.0 affy_1.24.2 [10] Biobase_2.6.1 limma_3.2.3 R.utils_1.4.0 [13] R.oo_1.7.2 R.methodsS3_1.2.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 cluster_1.12.1 grid_2.10.0 [4] lattice_0.17-26 preprocessCore_1.8.0 tools_2.10.0 Thanks in advance for any suggestions. Regards, Anupam -- Graduate Student, Center For DNA Fingerprinting And Diagnostics, 4-1-714 to 725/2, Tuljaguda complex Mozamzahi Road, Nampally, Hyderabad-500001 [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Hi Anupam, anupam sinha wrote: > Dear list, > I use the following code to process some cel files I have > : > >> dat<-ReadAffy() >> dat_norm<-rma(dat) > Background correcting > Normalizing > Calculating Expression >> dat_norm_mat<-exprs(dat_norm) >> > write.table(dat_norm_mat,"GSE3185.txt",sep="\t",row.names=T,col.name s=T,quote=F) > > and I get the following output in the text file : > GSM48598.CEL GSM48599.CEL > GSM48600.CEL GSM48601.CEL GSM48602.CEL > 100_g_at 3.47028618802937 3.49106274273872 > 3.46940719815954 3.46836687956259 3.45079245249753 > . > . > . > > I have couple of questions. > > 1) How do I add one more column to the text file which will give the gene > symbol for each of the probe-id ? library(hgu95av2.db) symbols <- unlist(mget(featureNames(dat_norm), hgu95av2SYMBOL, ifnotfound = NA)) out <- data.frame(symbols, dat_norm_mat) write.table(out, <you know="" the="" rest="">) Best, Jim > 2) Do the expression values get log2 transformed (after "rma" normalization > is done on the cel files or I have to perform it separately) ? > > This is my sessionInfo(): > R version 2.10.0 (2009-10-26) > i386-redhat-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] splines tcltk stats graphics grDevices datasets utils > [8] methods base > > other attached packages: > [1] WGCNA_0.89 Hmisc_3.8-0 survival_2.35-7 > [4] qvalue_1.22.0 flashClust_1.00 dynamicTreeCut_1.21 > [7] impute_1.22.0 hgu95av2cdf_2.5.0 affy_1.24.2 > [10] Biobase_2.6.1 limma_3.2.3 R.utils_1.4.0 > [13] R.oo_1.7.2 R.methodsS3_1.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 cluster_1.12.1 grid_2.10.0 > [4] lattice_0.17-26 preprocessCore_1.8.0 tools_2.10.0 > > Thanks in advance for any suggestions. > > Regards, > > Anupam > > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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