[BioC] matchrpobes and HGU95A mismatch

Saroj Mohapatra smohapat at vbi.vt.edu
Fri Oct 13 16:06:28 CEST 2006

I would also like to know the source of this discrepancy.

Some probe sets on the array did not make it to the hgu95aprobe package 
(or, so it seems to me). And I could not figure out why these probe sets 
were left out (e.g., excessive cross-hybridization?) However, it is 
possible to explore these probe sets at Netaffx.

Hope some one with more knowledge would weigh in ...


Ernest Turro wrote:
> Dear all,
> I downloaded the HGU95A CEL files from http://www.affymetrix.com/ 
> support/technical/sample_data/datasets.affx and installed the  
> hgu95aprobe matchprobes library, but they don't seem to match:
>  > length(pm(ReadAffy("CEL/hgu95a/1521a99hpp_av06.CEL")))
> [1] 201807
>  > length(hgu95aprobe$seq)
> [1] 199091
> Do any of you have any ideas what is wrong?
> Many thanks,
> Ernest Turro
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