[BioC] miRNA analysis advice

[Steve Lianoglou]

Hi Fiona,

On Tue, Feb 26, 2013 at 4:24 AM, Fiona Ingleby <fiona.ingleby at gmail.com> wrote:
> Hi James and Steve,
>
> Thanks very much for your advice, you've made things a lot clearer.
>
> There's just one more thing (for now!). I can think of two ways of going
> about a drosophila-specific analysis: I could either filter the data by
> species and test for differential expression only with drosophila probes, or
> I could just use the results I have already (for which I used a non-specific
> filter), but focus only on the drosophila subset of significantly
> differentially expressed miRNAs (to start with). I think James was
> suggesting the latter of these two, if I understood correctly, and this
> makes most sense to me (since the first method would mean completely
> disregarding a lot of potentially interesting probes), but I just wanted to
> check that this would be the best way to go about it.

One thing to note is that by removing the probes that do not belong to
the species you are interested in prior to running the differential
expression analysis, you will have more power to detect differential
expression in just the drosophila set of probes since you would be
reducing the number of multiple tests you need to correct for.

I think you said you had too many "hits" already, though, but perhaps
by doing so you can then add a second filter on the log-fold-change of
the differential expression, which maybe help to extract the stronger
changes in miRNA expression among the ones that are already called
significant by their adjusted p value.

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact