[BioC] Probe indices for the Drosophila2 Affy chip

[James W. MacDonald]

eblanc at ebi.ac.uk wrote:
> Thank you for your answer.
> 
> nrow( abatch ) returns 732 (as expected), but
> getOption("BioC")$affy$xy.offset returns 1 (instead of 0).

This is why you are getting differences between xy2i and xy2indices. The 
affy$xy.offset is there to allow you to use C-style counting (e.g., 
starting at zero) rather than R-style counting, which starts at 1.

I am not sure why your affy$xy.offset is being set to 1 - on both win32 
and linux I get 0, but maybe MacOS is supposed to be different. Anyway, 
I would stick with xy2i and friends.

Best,

Jim


> 
> Loaded libraries: affy version 1.4.32 and drosophila2cdf version 1.4.7 (in
> this order)
> 
> Thanks again,
> Eric
> 
> 

-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623