[BioC] matchrpobes and HGU95A mismatch

[Wolfgang Huber]

Dear Saroj & Ernest,

There is no implicit alignment between the output of the "pm" function 
and the rows of the probe packages.  pm returns all the PM probes of all 
probe sets, the probe package contains the sequences of the probes as we 
get them from Affymetrix. The two sets overlap, but are not the same.

The mapping of the rows of the probe package to the rows of the 
AffyBatch is via the hgu95acdf::xy2i function in the package hgu95acdf.

I think this is all fairly well documented in the man pages, please let 
me know if any documentation is missing.

  Best wishes
  Wolfgang.





Saroj Mohapatra wrote:
> 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 ...
> 
> Saroj
> 
> 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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> 
> 
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber