[BioC] Analyze miRNA experiment in Bioconductor

[Paul Geeleher]

Dear Members,

I've inherited a bunch of GenePix files from an miRNA experiment. They
are single color arrays, ( as opposed to 2 color as is the norm for
GenePix I think). There is a subset of 7 arrays and I wish to compare
a group of 4 of these to the other group of 3 and analyze differential
expression between the two groups. I was hoping somebody could point
me in the right direction of how I'd go about doing this with
Bioconductor? Is it possible using the Limma package? Is there any
code out there to assist me?

I've experience in analyzing Affymetrix data using Limma and PUMA, but
not GenePix, and the Limma Users Guide seems to focus on analyzing two
dye experiments.

I've uploaded one of the ".gpr" files to the net if anyone wants to have a look:

http://frink.nuigalway.ie/~pat/2007-02-19_130_0532.gpr

-Paul