Following the voom-limma workflow and using RNA-seq count data, I created the DGEList, ran the calcNormFactor (TMM) step, ran Voom step, and got the v object. I then extracted the $E object from v.
Here is my code:
x <- DGEList(counts=RNA)
x <- calcNormFactors(x, method = "TMM")
v <- voom(x, design, plot=TRUE)
My questions are: 1) expression profile in Elist has performed log(CPM) and been normalized for library size, right?; 2) Has the expression profile in Elist incorporated the precision weights (represented as $weights in v object) yet? Thank you.