[BioC] Duplicated probesets for the same gene

[Ye, Bin]

Hi, Saroj,

How have you been? 
As far as I know, the different probe sets are corresponding to different region of the gene, I don't know why Affy do this, probably they originally thought the probe sets for the same gene but different region will serve just like a "probe sets sets", a 2nd-layer confirmation of the gene expression, but it turned out sometimes the different probe sets of same gene express differently too. Sometimes it's because the probe sets are not all hybridize to the coding region of the gene, so when we do our analysis, we only consider the expression of the coding region probe sets, which, of course, take some "Blast".

Hope other experts can give better ideas about this!


Bin


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Saroj Mohapatra
Sent: Sun 4/23/2006 6:02 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Duplicated probesets for the same gene
 
Hi all,

I have a small curiosity regarding annotation of probesets in affy GeneChips. I find that some times 2 probe sets refer to the same gene.

For example, in the HG_U95Av2, there are 2 probesets (1369_s_at and 35372_r_at) both point to the same gene IL8. I wonder what is the scientific reason for such a duplication?

I understand that the signal from 2 probesets would be affected by dye-labeling effect and hybridization effect in addition to mRNA abundance. What is then the point of having 2 probe sets which might give different results for the same gene? 

Please send any pointers/references that you find appropriate.

Thanks for your consideration.

With thanks,

Saroj