[BioC] Duplicated probesets for the same gene

David Ruau druau at ukaachen.de
Mon Apr 24 15:12:35 CEST 2006

Affy spot spot multiple probeset of the same "gene". Especially when  
there is an extension like _s_at and _r_at meaning "similarity  
constraint" and "rules dropped" for the selection of the probes in the  
page 93-94 for more info.
Sometime they also spot multiple specific probeset _at for the same  
gene to measure the alternative transcripts.
But sometime probeset give different intensities even if the spot the  
same transcript. There could be multiple reasons for that, like the GC  
of the probe, the unspecificity of the mismatch probe, artifact on the  
chip etc...


On Apr 24, 2006, at 3:14, Sean Davis wrote:

> 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
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