Dear BioCommunities,

I'm new to RNA-seq. I have learned the batch correction method for this matrix here. And I also noticed that there was a chat indicated that this matrix is the normalized TPM values by RSEM (here).

But I'm still not sure whether the data type of this matrix, normalized counts, RSEM estimated counts, or TPM values by RSEM?

Besides,what's kinds of methods should be utilized for the differential expression analysis for this matrix? Thanks a lot!

All three tagged DE tools have extensive vignettes/manuals that cover recommended batch correction for the respective package.