[BioC] question about reading Affymetrix cel files

[James W. MacDonald]

James Anderson wrote:
> Hi, I am a new user of Bioconductor. I have a bunch of cel files from
> Affymetrix genechip. The gene expression data I used to work with
> have both the expression value and detection calls. Could somebody
> tell me how to convert cel files using bioconductor packages? My cel
> files are txt files, not binary files. I can read in the file using
> the package affy, but I don't know how to convert those files to the
> format I want to use (one column probe name, one column expression
> value, and one column detection calls (A,M,P), maybe there are
> another two columns, but they are not important).

If you want this sort of MAS5 output you can use the affystart() 
function in affycoretools with expression = "MAS5". This will output a 
text file containing the probe ID, expression value, detection calls and 
detection p-value.

affycoretools is in the devel repository, so if you are not using 
R-2.3.0 you will need to download by hand and install rather than using 
biocLite().

HTH,

Jim




-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623