[BioC] Re: Affymetrix - index of probes

[Benjamin Haibe-Kains]

Thanks a lot !
Affymetrix documentation seems to be not enough precise ...

James W. MacDonald wrote:

> Benjamin Haibe-Kains wrote:
>
>> Hi,
>>
>> I want to compare affy hgu133a and hgu133plus2 chips. When I retrieve 
>> the index of different probes on these two chips, the function 
>> indexProbes (see affy package) returns a list of 16 probes for the pm 
>> and 16 probes for the mm for each probe set.
>
>
> Not exactly true. There are some probesets with greater or less than 
> 11 PM probes, but in general there are 11 per probeset.
>
> > cdfName(dat)
> [1] "HG-U133A"
> > table(unlist(lapply(indexProbes(dat, "pm"), length)))
>
>     8    10    11    13    14    15    16    20    69
>     1     1 21748     4     4     2   482    40     1
>
> > cdfName(dat2)
> [1] "HG-U133_Plus_2"
> > table(unlist(lapply(indexProbes(dat2, "pm"), length)))
>
>     8     9    10    11    13    14    15    16    20    69
>     5     1     6 54130     4     4     2   482    40     1
>
> HTH,
>
> Jim
>
>
>
>>
>> However, we can see in the Affymetrix doument 
>> http://www.affymetrix.com/support/technical/datasheets/human_datasheet.pdf 
>>
>> that there are only 11 probes per probe set ! I don't understand the 
>> origin of the 5 exceeded probes ...
>>
>> Can you help me ?
>>
>> thanks
>>
>> NB: this email is maybe duplicated ...
>>
>
>

-- 
Benjamin Haibe-Kains

Licence in Computer Science
Master in Bioinformatics
Free University of Brussels (ULB)
E-mail: bhaibeka at ulb.ac.be 

MicroArray Unity
Institute Jules Bordet (IJB)
E-mail: benjamin.haibekains at bordet.be