You may also find this helpful: http://www.ark-genomics.org/events-online-training/working-affymetrix- cel-files Thanks Mick -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of WATSON Mick Sent: 30 October 2012 13:02 To: 'priya [guest]'; bioconductor at r-project.org; reddy.dhivyaa at gmail.com Subject: Re: [BioC] how to write into a proper textfile from CEL files ? Have you tried: library(affy) cel <- ReadAffy() pre<-rma(cel) ev <- exprs(pre) write.csv(ev, file="norm.csv") -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of priya [guest] Sent: 30 October 2012 12:39 To: bioconductor at r-project.org; reddy.dhivyaa at gmail.com Subject: [BioC] how to write into a proper textfile from CEL files ? I have a RMA normalized data ( from the CEL files ) and would like to write it into a file that I could open in excel but have some problems. library(affy) cel <- ReadAffy() pre<-rma(cel) write.table(pre, file="norm.txt", sep="\t") write.table(pre, file="norma.txt") The outut is arranged row-wise in the text file that is written using the above command and hence when exported to excel it is in a wrong form and many of the information is cut off as the maximum rows are used up .The output looks the following way : GSM 133971.CEL 5.85302 3.54678 6.57648 9.45634 GSM 133972.CEL 4.65784 3.64578 3.54213 7.89566 GSM 133973.CEL 6.78543 3.54623 2.54345 7.89767 How to write it in a proper format from CEL files in R to a notepad or excel ? -- output of sessionInfo(): R version 2. 15 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ 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 _______________________________________________ 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