I have been using DEseq2 for quite a while, but today I was looking a certain transcript and compared that to the raw counts, and found little login in the results. These are the output values:
log2FoldChange: 0.3434941483 pvalue: 2.16740140052804e-06 padj: 5.65192536063831e-06
These are the raw counts:
Treament A: 1878,644,3010 Treament B: 663,489,457
After RPM normalization I get these values:
Treament A: 993,996,1003 Treament B: 977,1001,961
With these values, one can hardly notice any change.. Could it be that DEseq2 is looking at the data in such a different way so the RPM values make little sense?