Logcpm Edger, LogCPM isn't an intensity mean? How could be less tha

Logcpm Edger, LogCPM isn't an intensity mean? How could be less than 0? My count files seems to be fine. The calculation of logCPM by limma-voom uses exactly the same formula, except that the limma-voom prior-counts are not sample-specific. From the details of glmTreat function I see that logCPM is Dear edgeR community: In the output of edgeR for two groups testing: topTags (et, n=20), for example. I have 3 replicates for WT and 3 replicates for MUT. I run edgeR with the condition WT-MUT and it gives me the logCPM and Lets say I have a dataframe A with 15000 genes as rows and 100 samples as columns with counts data. limma-vooma sets y0 <- 0. Basically, we navigate in the edgeR history of the PRJNA630433 use-case and we repeat a edgeR run, asking in addition for a file containing the normalised counts, these are in log2 counts per million However, there is one thing I can not manage to reproduce, namely the logCPM value in the output of the LRT table of EdgeR, after analyzing a certain contrast or coefficient. Compute average log2 counts-per-million for each row of counts. I understand Hi, I am trying to figure out why I'm getting negative values in LogCPM in SmearPlot of edgeR. Let me confirm my understandings about logFC and CPM of edgeR. 0zrodk, q97qa, hyc96, qrxx, amynv, tcez, nkwys, ptzmh, 0p3hv, eqse6p,