[BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix
mrobinson at wehi.EDU.AU
Thu Jul 17 09:48:29 CEST 2008
> 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,
To answer this part of your question, you can get the probeset.csv
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.
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
More information about the Bioconductor