What would a typical miRNA microarray analysis workflow look like?

Hi all,
What would a typical miRNA microarray analysis workflow look like? Say just a test group of 5 replicates from bladder cancer tumor and corresponding control group from normal tissue of the same patients. What could I do to make the analysis seems more sophisticated. I have done differential expression analysis, target gene prediction, and GO, pathway enrichments of target genes. What else could I do? It would be better if you can specify some packages or codes.
Regards,
Allen

PS: Is paired (t)-test necessery? I found that DE gene number from paired t-test is about half of that from normal limma functions( which I don't know how to do paired test if it could).

2014-08-26