[BioC] Re: a bug? non agreement btw. indexProbes and affy CDF file

James W. MacDonald jmacdon at med.umich.edu
Mon Nov 1 17:30:53 CET 2004

ulas karaoz wrote:
> Why these indices are offset by 1 compared to yours, has this anything 
> to do with the package wide xy.offset = 1 option?
> I am very puzzled about what are the correct indices, can I plug in 
> simply the indices from the CDF file, which seem to be computed as: x+ 
> (712 * y) for U133A chip. Clearly I am missing something.
> thanks.

Rafael and Laurent would know better than me, but I think the difference 
is due to different indexing between R and most other programming 
languages. R indexes starting at 1, whereas most other languages start at 0.

BTW, I get a different offset than you.

 > unlist(getOption("BioC"))$affy.xy.offset
[1] 0



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

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