[BioC] Limma final gene expression report

[Ankit Pal]

Dear Sean,
I agree averaging is not a good idea.
So how do I get a single value for a set of replicate
probes?
In case of different values for the same gene which
result do I consider to be representative of the
whole?
It would definately help at the clustering level.
-Ankit
 
--- Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 
> 
> 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
> 
> 


		

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