[BioC] how to write into a proper textfile from CEL files ?

[WATSON Mick]

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 at r-project.org [mailto:bioconductor-bounces at 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") 


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-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at 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

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