Hello everyone! I want to analyze together the gene expression profiles from two different datasets and compare a number of genes between the two. One of them is in rsem v2 output format, and the other in fpkm (cufflink output). I have triend calculating the fpkm from rsem raw counts, but the distributions do not correlate at all so I am not sure if it would be possible to compare the gene expression among them as the data do not seem to be in the same scale.
Do you have any idea if it is possible to make these two data type comparable?
Thank you in advance,