Differential gene expression analysis with RPKM
1 answer
Ask for raw counts or if you do not have anything else than RPKM (or any other values that hopefully are somewhat properly normalized) then use limma-trend after transforming values to log2 scale, see section 15.4 of the limma user guide.
In the future please use the search function, this has been asked a lot of times before.
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I did find the limma method online. I was wondering if there are other methods available. Since I can't get the raw counts, I guess I have to report the limma method even though it is not ideal. Thank you!