[BioC] Probe indices for the Drosophila2 Affy chip

[Eric Blanc]

Dear List,

I have problems understanding probe indices for the Drosophila2 chip: 
the xy2indices and xy2i functions return different values, and I 
couldn't find anywhere whether either of them has been deprecated. xy2i 
seems to return indices compatible with pmindex, mmindex and probeIndex 
functions. (I made sure that the indices from the functions pmindex, 
mmindex and indexProbes were self-consistent and they are. The MM index 
always is 732 greater than its corresponding PM index).

Also, the number of indices returned by the pmindex, mmindex and 
probeIndex functions is 42 less than the number of probes in the 
drosophila2probe data frame. All probes from sets "AFFX-Dm-pd2EGFP_at", 
"AFFX-Dm-pAsRed2_at" and "AFFX-Dm-pDsRed-Exp_s_at" seem to be missing. 
I don't know why they don't come up, as they aren't those which have an 
even y coordinate (only 180 probes in 9 probesets or 20 probes each).

So my questions are:

1) Can you confirm that xy2i and i2xy are indeed the functions to use 
instead of xy2indices and indices2xy ?
2) Is there anything wrong with the 3 missing probe sets that I should 
know ?


platform powerpc-apple-darwin7.4.0
arch     powerpc
os       darwin7.4.0
system   powerpc, darwin7.4.0
status
major    1
minor    9.1
year     2004
month    06
day      21
language R

affy version 1.4.32


Thanks very much for your help,
Eric

--
Dr. Eric Blanc						e-mail: eblanc at ebi.ac.uk
European Bioinformatics Institute		Tel: +44 +1223 492 537
Wellcome Trust Genome Campus			Fax: +44 +1223 494 468
Hinxton - Cambridge CB10 1SD
- UNITED KINGDOM -