Is there a way to obtain the CPM values from EdgeR after batch correction? The "cpm" function only returns values after library size normalization. When I look at the result of glmFit there are "abundance" "fitted.values" and "counts". The description in the documentation (?glmFit) is not entirely clear to me. Are the "fitted.values" cpm values after batch correction or should I be doing something else?
Thanks!
Thanks!
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