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

Mark Robinson mrobinson at wehi.EDU.AU
Thu Jul 17 09:48:29 CEST 2008

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:

The PGF/CLF can be found at:

Look for "Mouse Exon 1.0 ST Array Analysis (zip, 114 MB)", which after  
logging in, will get you:

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.


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

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