Hi Peng, On Nov 10, 2009, at 8:53 PM, Peng Yu wrote: > On Tue, Nov 10, 2009 at 2:21 PM, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: >> Hi, >> >> On Nov 10, 2009, at 3:17 PM, Peng Yu wrote: >> >>> I currrently use the following code to generate RMA results (in >>> exprs.txt). But it is inconvenient to save a text file. If I can >>> save >>> the result in '.RData' format, it would be faster. I'm wondering >>> what >>> variable in 'eset' I should 'save()' into '.RData' format. >>> >>> library(oligo) >>> cel_files = list.celfiles('.', full.names=T,recursive=T) >>> data=read.celfiles(cel_files) >>> eset=rma(data) >>> write.exprs(eset, file="exprs.txt", sep="\t") >> >> It shouldn't be different than saving another other R object: >> >> save(eset, file="exprs.eset.rda") > > 'eset' has a lot of things that I don't need. I only want to save the > RMA corrected expression values that were in 'exprs.txt' to a '.RData' > file. I'd suggest reading some of the introductory vignettes you have access to when you load the affy library. In particular, check out the "Primer", and "An introduction to Biobase and ExpressionSets". You'll find it quite helpful down the road if you get familiar with working with ExpressionSets, etc. now (it can be a pain at first). So, you'd do: ... eset <- rma(data) expr.matrix <- exprs(eset) save(expr.matrix, file="exprs.rda") ... HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

exprsData = exprs(eset) save(exprsData, file="fileName.rda") b On Nov 10, 2009, at 11:53 PM, Peng Yu wrote: > On Tue, Nov 10, 2009 at 2:21 PM, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: >> Hi, >> >> On Nov 10, 2009, at 3:17 PM, Peng Yu wrote: >> >>> I currrently use the following code to generate RMA results (in >>> exprs.txt). But it is inconvenient to save a text file. If I can >>> save >>> the result in '.RData' format, it would be faster. I'm wondering >>> what >>> variable in 'eset' I should 'save()' into '.RData' format. >>> >>> library(oligo) >>> cel_files = list.celfiles('.', full.names=T,recursive=T) >>> data=read.celfiles(cel_files) >>> eset=rma(data) >>> write.exprs(eset, file="exprs.txt", sep="\t") >> >> It shouldn't be different than saving another other R object: >> >> save(eset, file="exprs.eset.rda") > > 'eset' has a lot of things that I don't need. I only want to save the > RMA corrected expression values that were in 'exprs.txt' to a '.RData' > file. > > _______________________________________________ > 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