[BioC] read subset of affy data

[Rafael A. Irizarry]

you can use read.probematrix directly (its what justRMA calls). 
it reads either only pm, only mm, or both without creating an
AffyBatch.


On Sat, 18 Oct 2003, James MacDonald wrote:

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