I am new to the field of RNASeq and I have been reading a lot on different normalizations etc. on Biostars but I couldn't find an answer to the problem I am facing right now:
I have a data set from this paper (dx.plos.org/10.1371/journal.pone.0118528) and as far as I understand it, they used TMM normalization:
Samples were grouped and quantification of transcript abundance was performed on this final read list using Trimmed Means of M-values (TMM) as the normalization method . Output data utilized for all subsequent comparisons was a normalized signal value generated by AvadisNGS.
Now I want to compare this data with a dataset of TCGA which uses RSEM (https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2).
I found some posts on similar questions (e.g. TMM normalisation from RSEM raw counts) but I still don't know how to proceed. Can anyone help me out?
Thank you so much!