[BioC] pmindex

[Laurent Gautier]

I do not think that one should rely on the ordering of the probes 
returned by indexProbes (or wrappers). I think that if there is an 
ordering of some kind for certain chip types, it might well be accidental.

In the official 'cdfenvs', the ordering of the probes in the probe set 
is simply done according to the 'ATOM' number in the CDF file (no public 
doc about Affymetrix file formats when the parsers were written, I just 
checked and the newly existing docs only say: "ATOM: integer value 
assigned to the probe pair"... ).

Of course, in the case I am wrong I will be publicly corrected here. :)



L.


Wenbin Liu wrote:
> Dear Bioconductorians,
> 
> Can someone tell me if the returned index by pmindex()
> ordered by the position of the probes on the target
> sequence? If so, is it from 3' to 5' or the other way?
> Here's an example of the result:
> 
> $"1423504_at"
> [1] 886892 626949 262157 850850 892792  91807 312389 
> [8] 923026 993970 231493 316615
> 
> 
> Thanks a lot!
> 
> Wenbin
> 
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