[BioC] Duplicated probesets for the same gene

[Sean Davis]

Saroj Mohapatra wrote:
> 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?

There can be a number of reasons for such duplication.  The first and 
foremost is probably that we are typically measuring "transcript" 
expression rather than gene expression, except in the case that there is 
only one transcript for a given gene.  If there is more than one 
transcript, it may be necessary to have more than one probeset to 
capture all of them.

I would say that in general, most modern arrays cover many genes more 
than once; one can certainly not make any assumptions about each gene 
being represented only once.

> 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?

They often give similar results, but sometimes not.  A certain amount of 
redundancy is probably a good thing, although it can be a headache.

Sean