(or Celine... the signature makes me confused about which name to use)
I have never used any 2-genome-chip with only one genome,
but I have been working on something (revised submission pending... I
could send a pre-print if interested) that could be of help for you.
If think you would need to create a special cdfenv.
The package 'altcdfenvs' contains helping functions to
play with mappings (althought not enough to have a 'one-call' in your
If you want to rely on the original probe
sets, just keep in the environment the ones concerning
one of the two genomes. If the affy IDs contains in their name a hint
about the genome they belong to, this can be done in wink (apparently
this is the case, the IDs starting
with 'Pf' are likely to belong to Plasmodium).
altcdfenvs-devel will hopefully contain functions to cover
this case in the near future.
Hoping it helps,
On Tue, 2004-06-08 at 18:06 +0100, Jason Skelton wrote:
> I would like to know if anyone used the Anopheles/malaria Affymetrix
> chips in bioconductor or any other 2-genome-chip but hybridising
> one genome only? I do, and hybridise with 1 species only, resulting
> problematic normalisation procedure.
> I tried Affy, simpleaffy and affylmGUI, and can't manage to have
> statistics while I have no problem at all using a 1 species chip.
> suggestion would be largely appreciated.
> Thanks a lot