[BioC] Affymetrix Human Gene 1.0 ST Array

Crispin Miller CMiller at picr.man.ac.uk
Thu May 8 11:55:57 CEST 2008

RE exonmap... The package offers annotation mapping from probeset locations
(we annotated the arrays against the whole genome) to the genes, transcripts
and exons at that position, along with mappings between the different levels
of annotation).

I'm not sure how useful it would be in the context of Gene level arrays -
but given a gene symbol or genomic location, it should be straightforward to
map to the corresponding transcripts and exons.

The easiest way to see what information is represented in the package is to
have a look at the accompanying genome browser at:



On 7/5/08 19:44, "Hans-Ulrich Klein" <h.klein at uni-muenster.de> 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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