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.

Many thanks again,

Fiona


Dr Fiona C Ingleby
Postdoctoral Research Fellow 
University of Sussex



On 25 Feb 2013, at 16:34, Steve Lianoglou <mailinglist.honeypot@gmail.com> wrote:

> Hi,
> 
> On Mon, Feb 25, 2013 at 10:25 AM, James W. MacDonald <jmacdon@uw.edu> wrote:
> [snip]
>> In general I like to see somewhere around 15-30 differentially expressed
>> miRNA transcripts, as anything more can become quite intractable for the
>> people I collaborate with. This is because each miRNA may target > 1000 mRNA
>> species, so too many miRNAs and all of a sudden every gene might be a
>> potential target.
> 
> ... and don't forget to model competing endogenous RNA (ceRNA) effects!
> 
> -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


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