[BioC] how to do the following using justRMA in affy package?

Seth Falcon sfalcon at fhcrc.org
Fri May 11 16:03:07 CEST 2007

James Anderson <janderson_net at yahoo.com> writes:

> Hi,
> I have 100 cel files (U133A) in a folder, I want to randomly select 70
> cel files from them and use justRMA to get the normalized intensity. I
> need to do this 50 times (every time, the 70 cel files are not
> necessarily the same). More imporantly, I want to save the expression
> value obtained by justRMA to file name Data_1.txt Data_2.txt
> Data_3.txt, ..., Data_50.txt in an automatic fashion. I tried myself
> first and could not figure out how to do it, could anybody offer me
> any help or suggestions?

Try reading the help pages for these functions:


for (i in 1:50) {
  Create a character vector of your 100 CEL files.  
  Sample 70 elements.
  Run justRMA
  save to file paste("data_", i, ".txt", sep="")

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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