I would like to use edgeR for differential Gene expression analysis.
I have read counts data on 50 individuals in three biological replicates.
I would like to filter out lowly expressed genes. Is there a threshold to define express genes?
I was thinking to use CPM of >=2, and it should be in two of the three libraries.
How do I define R code?
Secondly, I would like to output TMM normalized counts to identify uniquely expressed genes in each of the individuals. How do I output the TMM counts in CPM?
Thanks in advance