[BioC] difference between hgu95av2probe library and pm matrix

Laurent Gautier laurent at cbs.dtu.dk
Fri Sep 19 10:12:21 MEST 2003

On Thu, Sep 18, 2003 at 11:37:37AM +0200, M.Ruschhaupt at dkfz-heidelberg.de wrote:
> Dear all, 
> I have just started to work with R and Bioconductor. Now I have a question about 
> the hgu95av2probe library and also the hgu95probe library. Does anybody know, why 
> not all probes are listed there.   

These two packages are built from the "probe information files" made
public by Affymetrix (and available on the company's website).

> For example the pefect match matrix in the Dilution affy batch object from the 
> affycomp package is an matrix with 201800 rows (probs) but the hgu95av2probe object only 
> has 199084 rows. So there is a difference of about 2700 probes. Is their sequence unknown or 
> why are these probes not listed in hgu95av2probe ? 

If you know, please share the information.
My guess (from some work I have done with that) would be that some probes
were found to be not so good and were removed from the revised u95a chips.

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.  

Hopin' it helps,


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

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