[BioC] Read single channel GenePix in limma [was: Analyze miRNA experiment in Bioconductor]

[Gordon K Smyth]

Dear Paul,

I have no experience with miRNA arrays, so cannot give you any specific 
advice.

With ordinary expression arrays, my practice is to keep the probes 
separate, especially if they actually have differing sequences.  There's 
no good summarisation method which feeds into the topTable format.  I 
convert to genes or transcript only at the interpretation stage.  The only 
exception are within array replicates which satisfy the (restrictive) 
assumptions of the duplicateCorrelation() function.

Best wishes
Gordon

On Wed, 14 May 2008, Paul Geeleher wrote:

> Hi Gordon,
>
> Thanks for you email. I've followed your steps and am getting some output now.
>
> One problem though. When should the summarization step occur? What I
> mean is that, between miRNA and control signals, my GPR file contains
> about 3000 entries and when I am done with analysis topTable will
> return all of these individually. But many of the miRNAs have multiple
> entries in the ".gpr" file. So how, and when, should I go about
> combining these into one value?
>
> Thanks in advance,
> -Paul