[BioC] Analyze miRNA experiment in Bioconductor

[Deepayan Sarkar]

On 5/6/08, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> 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.

Any analysis ultimately boils down to some sort of normalization, and
the actual differential expression analysis. The second part in limma
(lmFit, etc.) can work with any expression matrix, irrespective of
whether it's 2-color or 1-color (or affy).

We have been working with a miRNA array dataset recently, and we used
limma to read in the GPR files and do the differential expression
analysis (on one channel). For normalization, many of the standard
microarray algorithms probably don't make much sense, but VSN seems to
work fine.

We don't really have code (beyond what's already in limma and vsn)
that is generally useful; most of the work is in figuring out which
rows are of interest (i.e., those representing human miRNAs),
combining the replicates (you seem to have four of each), etc. I'm
happy to give you more details if you are interested.

-Deepayan