[BioC] read subset of affy data

James MacDonald jmacdon at med.umich.edu
Sat Oct 18 21:16:20 MEST 2003

Look at the code for justRMA in the release version of affy. It is much
less memory intensive to iteratively put a cel file in an affybatch,
extract the PM data to a matrix and then overwrite the affybatch with
the next cel file. You could easily modify the code to only extract the
PM data you are interested in into the matrix.

Alternatively you could simply use justRMA to get expression values and
go from there.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> Xuejun Peng <xpeng at bio.ri.ccf.org> 10/17/03 19:22 PM >>>
I have 100 affy arrays and I got an "out-of-memory" error message when I

try to batch-read all of them simultaneously. On the other hand, it is 
really inefficient to read them one by one.
Since I have a specific list of genes that I want to read, can I use 
ReadAffy or some other functions to read the subset of genes directly 
from .cel files? For a simple example, I only want to read  five genes 
and I know their probe set ID's.

Can anyone help? Thanks.


Xuejun Peng, Ph.D.
Assistant Staff
Biostatistics and epidemiology / Wb4
Cleveland Clinic Foundation
9500 Euclid Avenue
Cleveland, OH 44195
Phone: 216-444-9958
Fax: 216-444-8023
E-mail: xpeng at bio.ri.ccf.org, pengx at ccf.org

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