Dear all,

I am working with microRNA data and as it is very new to me, I have some general questions. I'm hoping that some people on this list who know more about microarray analysis and miRNA than myself might be willing to offer some opinions/advice.

First, when doing quality checks on the data, how useful is it to look at the RNA degradation plots with miRNA, given how short miRNAs are?

Second, when analysing differential expression (using lmFit and eBayes in the 'limma' package), I find quite high numbers of probes which are significantly differentially expressed across my samples (in some contrasts as many as ~500 out of 4000 probes are significantly differentially expressed between samples). Is this unusual with miRNA data? Further, although a lot of these probes are from Drosophila species (which I expected since my samples are from D. melanogaster), some are from other insects, and even other phyla (there are some C. elegans and human miRNA probes which are found to be significantly differentially expressed, for example). 

>From what I have read in the literature so far, there does seem to be some conservation of miRNAs between diverse species, but I can't find any information about to what extent I might expect to find this in my data. I'm a little concerned that this level of homology between species might be unusual, which would suggest that I've made a mistake in the analysis.

As I said, I am very new to this, so if anyone is willing to offer advice or just point me in the direction of some useful information I could look at myself, then I would really be very grateful.

Many thanks in advance,

Fiona

Dr Fiona C Ingleby
Postdoctoral Research Fellow 
University of Sussex, UK


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