[BioC] Affymetrix Human Gene 1.0 ST Array

Hans-Ulrich Klein h.klein at uni-muenster.de
Wed May 7 20:44:19 CEST 2008

Dear List,

I would like to analyze Hume Gene 1.0 ST Arrays using BioC. I am 
interested in differential expression at probeset and at gene level. 
Searching the list archives reveals, that "makecdfenv and 
makePlatformDesign make the assumption that there is a one-to-one 
mapping of probe ==> probeset", which is not true for the Human Gene 1.0 

Anyway, I found some interesting packages:
- exonmap: Looks promising, but there are no cdf files for the Gene 1.0 
Chip on the related website (just for the Exon 1.0)
- xps: This seems to be a completely new infrastructure for affymetrix 
chips, which is capable of reading the Gene 1.0 Chip.
- aroma.affymetrix: This is not a BioC package. (Why not?)

Have I overseen a package? Can someone point me to further information 
regarding BioC and the Human Gene Chip? I am not sure where to start and 
appreciate any comments and experiences of other users.

Best wishes,

PS: Is there any work going on the integration the Human / Exon Chip in 
the affy packages? Or are these Chips too different from the 
conventional 3' Chips.

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