I'm dealing with a set of sequencing data with batch effects. The samples were sequenced at two different times (4 control + 4 treatment1 at the first time, and 1 control + 4 treatment2 at the second time). The batch effects are very obvious when I looked at the PCA plots of raw data. I used RUVSeq and edgeR and fitted the linear model with batch effects included in the design. The results are OK, but I cannot find a way to look at the counts without batch effects. Even the counts in fit$fitted.values are still with batch effects.
So, I'm wondering is it possible to get the counts without batch effects after linear model fitting? I need these counts for making heatmap. I found someone said this in an old post - getting a matrix of batch corrected counts is not possible. If the counts do not exist, how are logFC and logCPM calculated (they are batch effects free in my results)?
Or this can be done by other packages like DESeq?
Or I should use removeBatchEffect function just for making heatmap?