I have used
limma trend to find DE genes between 3 groups (including batch effect in design). Now I would like to visualize the genes, and used
removeBatchEffect() to get corrected logCPM values for each sample.
logCPMc <- removeBatchEffect(logCPM, batch=targets$Batch, design=design_4_batch)
Now I want to use the average of each group, and with
edgeR, I don't see a way to include this batch effect. What would be the correct way to get these average log2 CPM values with batch effect removed? Averaging the logCPMc (batch corrected) values would not be correct, right?