[BioC] difference between hgu95av2probe library and pm matrix

[Laurent Gautier]

On Fri, Sep 19, 2003 at 09:55:25AM +0200, M.Ruschhaupt at dkfz-heidelberg.de wrote:
>  
> > 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. 

I think one has to go to the annotation for these probes. For the particular
example you give, the information available are:
(copy/paste from http://www.medfac.leidenuniv.nl/lgtc/db/Affy/HG-U95A.txt)
HG-U95A	1142_at	HG3432-HT3618	"Fibroblast Growth Factor Receptor K-Sam, Alt. Splice 1"	 	individual sequence
HG-U95A	1143_s_at	HG3432-HT3620	"Fibroblast Growth Factor Receptor K-Sam, Alt. Splice 3, K-Sam III"	 	group members not included
HG-U95A	1144_at	HG3432-HT3621	"Fibroblast Growth Factor Receptor K-Sam, Alt. Splice 4, K-Sam IV"	 	individual sequence
HG-U95A	1145_g_at	HG3432-HT3621	"Fibroblast Growth Factor Receptor K-Sam, Alt. Splice 4, K-Sam IV"	 	group members not included


I shall be able mail a little more about alternative splicing and
Affymetrix probes within the very near future (hopefully).


L.



>  
> Markus 

-- 
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent