[BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix

[Mark Robinson]

Hi An.

> With respect to xps, your reference to script4xps.R is really  
> helpful.  Do you have a URL from where the files "MoEx-1_0-st- 
> v1.r2.clf", "MoEx-1_0-st-v1.r2.pgf", "MoEx-1_0-st- 
> v1.na25.mm9.probeset.csv", "MoEx-1_0-st-v1.na25.mm9.transcript.csv"  
> can be downloaded?  I searched on the Affy site but did not find it,  
> sorry.

To answer this part of your question, you can get the probeset.csv  
file from:
http://www.affymetrix.com/analysis/downloads/current_exon/

The PGF/CLF can be found at:
http://www.affymetrix.com/support/technical/libraryfilesmain.affx

Look for "Mouse Exon 1.0 ST Array Analysis (zip, 114 MB)", which after  
logging in, will get you:
MoEx-1_0-st-v1.r2.zip

There are plans to make a couple versions of Mouse CDFs for use with  
FIRMA within aroma.affymetrix.  I'm not sure when that will actually  
be, but hopefully "soon".


> Does xps work with AffyBatches?  If not, is it possible to create an  
> AffyBatch with the raw data?


xps, from my limited experience with, does not deal directly with  
AffyBatch objects, but maybe you can export one.

Cheers,
Mark



------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852