[BioC] matchrpobes and HGU95A mismatch

[Ernest Turro]

Dear Wolfgang,

Thanks for your response.

The issue here isn't about aligning the output of the affy functions  
with the output of the matchprobes packages. I was wondering why some  
of the probe sequences are missing from the hgu95aprobe package (167  
probesets-worth of sequences, if I recall correctly). Is this common?  
I've worked with the hgu133atagprobe and drosgenome1probe packages  
before and they both had sequence information for all the probes in  
their respective CEL files.

Thanks in advance for clarifying this for us.

Best,
Ernest


On 24 Oct 2006, at 23:07, Wolfgang Huber wrote:

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