Hi,

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

**function (**

*ScaleData**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?

Thank you Kevin. I will try it.

I believe it should be

according to here: Multi-Factorial Differential Expression Analysis

Thank you - I have edited the answer.