[BioC] matchrpobes and HGU95A mismatch

[Robert Gentleman]

Hi,
   Pretty much we just transform what Affymetrix puts up (and that 
changes from time to time). So, if you download the appropriate files 
from Affymetrix and find that indeed they have a different number of 
sequences than we are reporting, then please file a bug report. 
Otherwise, I am afraid it is a question for the Affymetrix help desk. 
But there is a reason that there are two different chip IDs, so I would 
not expect the sequences, or even the number of sequences to be the same.

   The same goes for lots of other files from them (or other sources), 
we can only report/translate what they give us. There is no independent 
way for us (or anyone, AFAIK) to figure out what the sequences were. And 
we don't purposefully leave anything out. The process is semi-automated 
and bugs can creep in, but we are pretty careful about testing.


  best wishes
    Robert


Bao Cao wrote:
> Dear All,
> 
> I've been very interested in this question when I was searching the list. 
> Anybody has any conclusion on this? Could we discuss more here please?
> Thanks in advance.
> 
> Best,
>  Cao
> 
> 
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at ...
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/ 
>>>> gmane.science.biology.informatics.conductor
>>>>
>>> --------------------------------------------------------------------- 
>>> ---
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at ...
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/ 
>>> gmane.science.biology.informatics.conductor
>>
>> -- 
>> ------------------------------------------------------------------
>> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at ...
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor 
> 
>  __________________________________________________
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org