I would like to run differential expression analysis on my single-cell data. My data contains of 5 groups which sequenced in 3 batches. Each batch contains all of the groups. Before the differential expression analysis with monocle (I should run it with monocle) I have tried to eliminate batch effect from the data. I used Seurat's ScaleData function (vars.to.regress argument) to regress out the batch effect. However, the output of this function is in scale format which contains negative values in it.
Can I use scale values in differential expression analysis, specifically monocle?
I also tried limma's removeBatchEffect function, which also gives negative values. What is the best way to regress out the batch effect before the monocle differential expression?