[BioC] help with array based microRNA data analysis

[Abhishek Pratap]

Hey Guys

We have some custom array based microRNA data scanned using GenePix
4000B scanner and stored in gene pix results (gpr file format).

In this case it is not necessarily case-control study as all of our
samples are actually with the disease. Our plan is to first generate a
simple matrix of normalized expression across all the samples.

 To do this I would appreciate if anyone can point me to similar
analysis/papers done in the past or Bioconductor packages that could
help out.

I did look at limma but not sure if it is recommended for microRNA and
plus we dont want to do differential expression at this point.

Thanks a lot for your time!
-Abhi