[BioC] Limma final gene expression report

[Sean Davis]

On May 10, 2005, at 6:54 AM, Ankit Pal wrote:

> There are different oliogos of the same gene and
> replicates with the same sequence present on the
> array.
> Splice variants have been mapped to the same Accession
> number but I'm working on that to separate out the
> same by naming them differently.
> -Ankit
>

So, for the different oligos/splice variant spots, averaging is 
probably NOT a good idea in most situations--they could be measuring 
quite different things.  When there is a discrepancy, it MAY be due to 
array issues (quality of one spot, for instance), but it could also be 
a true finding; determining which is which often requires some human 
intervention.

Perhaps others will weigh in on the issue, but I don't think ad-hoc 
averaging of truly duplicated spots really serves a purpose, either.  
Unless your array design allows you to treat the duplicated spots at 
the level of the analysis (lmFit, in limma) and not post-processing, I 
don't think you benefit much from averaging (i.e., you don't have more 
"confidence" in a gene that has been averaged).

Sean