I have a conceptual question that I was hoping someone could answer.
Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after normalizing the data? Does it matter if I use RSEM or RPKM values. It seems to me that it should be legitimate in any case since microRNAs are approximately the same length, but maybe I am overlooking something.
For example, I am following a paper published in Nature Communications entitled "Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif". The authors download the data and collapse isoform reads to a single read count using the reads. They say they used the reads per million microRNAs mapped, which establishes each microRNA read count as a fraction of the total microRNA population. The authors then do upper quartile normalization which they say is important because a subset of microRNAs (miR-143 in particular) contributes so significantly to the total read count. In the text, the authors appear to use the resulting values to do a direct comparison between microRNAs.
I definitely want the collapsed isoforms, and I think it makes sense to do the normalization. However, I would like to say that a particular microRNA is expressed x-fold higher than another. Can I do this from the collapsed and normalized data?
If this has already been answered, I apologize. I could not find it. Thanks.