[BioC] Affymetrix Human Gene 1.0 ST Array

cstrato cstrato at aon.at
Wed May 7 23:59:14 CEST 2008

Dear Hans-Ulrich

Although I think that there is a cdfenv for the HuGene array, which can 
be used with 'affy', it may always be a good idea to try different packages.

I believe that for the HuGene array my package 'xps' may have some 
- it parses the original Affymetrix CLF, PGF and annotation files
- in addition to RMA normalization you can also do DABG and even MAS5 
detection calls
- it works on computers with 1GB RAM only

In  any case I would be very interested in user's feedback, and would 
appreciate if you would give it a try.

Best regards
C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
V.i.e.n.n.a       A.u.s.t.r.i.a
e.m.a.i.l:    cstrato at aon.at

Hans-Ulrich Klein wrote:
> 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 chip.
> 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,
> Hans-Ulrich
> 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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