[BioC] Affymetrix - index of probes

[James W. MacDonald]

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 ...
> 


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109