[BioC] Probe indices for the Drosophila2 Affy chip

James W. MacDonald jmacdon at med.umich.edu
Tue Aug 9 15:14:27 CEST 2005

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.



> 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

More information about the Bioconductor mailing list