[BioC] difference between hgu95av2probe library and pm matrix

[M.Ruschhaupt at dkfz-heidelberg.de]

> Quantifying the differences would be a cute example to show the 
> flexibility 
> of the 'affy' package... it is not a too difficult thing do 
> (hint: make use of the corresponding cdfenv packs). 
> Do not hesitate to share your code.   
>  
Here is the code I used to see, which probes are not listed in the hgu95av2probe object. It is 
far away from being efficient and the difference is only checked for the Dilution set of the 
affycomp package but that should not matter. 
 
> load("Dilution.rda") 
> library(hgu95av2probe) 
>  p.index <- xy2indices(hgu95av2probe$x+1,hgu95av2probe$y+1,ab=Dilution) 
> length(p.index) 
[1] 199084 
>  ind <- unlist(indexProbes(Dilution, "pm")) 
> length(ind) 
[1] 201800 
> ind2 <- ind[! ind %in% p.index] 
> length(ind2) 
[1] 2716 
> ind2[1:5] 
1142_at1 1142_at2 1142_at3 1142_at4 1142_at5 
  387228    17915   239242   334935    48584 
 
Maybe this can help to find out why these probes are not in the hgu95av2probe object. 
 
Markus