[BioC] select probe pairs for expression index

Rafael A. Irizarry ririzarr at jhsph.edu
Fri Apr 4 16:27:46 MEST 2003

yes its possible. the easiest way is to create a new cdf environmet that 
excludes these. some details:

1 -  the hash tables in the cdf environmets contain a J x 2 matrix with 
the PMs locations in the exprs slot matrix in the first column and the MMs 
in the second. J is the number of probes (typically 16 in the hgu95a chip)

2- the order in which they appear are the given by "probe number". so all 
you do is take out the first 5 entries.

3- the cdfName slot in AffyBatch tells the affy package where to find the 
PM and MM information. once you define the new cdf package or environment 
you stick the name of the environmnet or package in the cdfName slot.

4- normalization and bg correction will only be done on these probes

Leslie Cope (cc-ed) and I are actually working on somehting similar. We 
will soon have software that automatically does this.


On Thu, 4 Apr 2002, Sek Won 
Kong, M.D wrote:

> Hi, Bioconductor
> For affy package, is it possible to calculate expression index with part of probe pairs?
> For example, I want to focus on probe pairs # 5 - 16 instead of #1 -16 and discard the informations from first four probe pairs.
> Thanks!
> -SW
> 	[[alternate HTML version deleted]]
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