I just summarized a dataset using the expresso() function. I then normalized the data using limma's "normalizebetweenarrays()" function. But now I need to pull out just the miRNA data from everying else on the chip...and while i have a list of miRNA transcript names, I have rownames such as "14qI-8_x_st" or "14qI-9_x_st " rather than "hsa-let-7e-5p" etc.
How do I go about getting actual TRANSCRIPT expression values out of what I have? the oligo package seemed to do this automatically, but I can't use that as Im trying to run cyclic loess normalization and I dont think it has that.
Anyway, I'd be greatful for any help. I hope this post made sense...its very late.