[BioC] read subset of affy data

[Rafael A. Irizarry]

i forgot to mention, this is in the devel version.


On Sat, 18 Oct 2003, Rafael A. Irizarry wrote:

> 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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> 
>