[BioC] Limma final gene expression report

[Sean Davis]

On May 10, 2005, at 7:45 AM, Ankit Pal wrote:

> 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?

That is the problem, isn't it.  If you have duplicate spots (same 
sequence), you will need to look at the quality, etc., to see which you 
believe.  If you have oligos that map to the same gene but behave 
differently, you will need to look at spot quality as well as other 
issues like the cross-hybridization potential (which often requires 
blasting), location in the gene (3' bias?), and splice variants that 
may be tissue specific.  As I said, all of these require a bit of human 
intervention.  In practice, though, you have to validate array results 
biologically--that is the real answer to your question.  The 
"representative" spot is the one that validates; sometimes that will be 
the one that suggests differential expression, and sometimes not.

Sean


> It would definately help at the clustering level.
> -Ankit