Hello everybody, I would like to know if anyone used the Anopheles/malaria Affymetrix chips in bioconductor or any other 2-genome-chip but hybridising with one genome only? I do, and hybridise with 1 species only, resulting in a problematic normalisation procedure. I tried Affy, simpleaffy and affylmGUI, and can't manage to have good statistics while I have no problem at all using a 1 species chip. Any suggestion would be largely appreciated. Thanks a lot Celine

Jason, (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 particular case) 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, L. On Tue, 2004-06-08 at 18:06 +0100, Jason Skelton wrote: Hello everybody, > > I would like to know if anyone used the Anopheles/malaria Affymetrix > chips in bioconductor or any other 2-genome-chip but hybridising with > one genome only? I do, and hybridise with 1 species only, resulting in a > problematic normalisation procedure. > I tried Affy, simpleaffy and affylmGUI, and can't manage to have good > statistics while I have no problem at all using a 1 species chip. Any > suggestion would be largely appreciated. > Thanks a lot > > Celine