I have counts data for 18 samples, two conditions, sequenced in two batches. I would normally run DE analysis with batch as covariate.
A density plot on the scaled CPM data shows a bimodal distribution. Density plots of the separated batches show single peak more-or-less normal distributions so my conclusion is that the bimodality is caused by the batches.
I know that for running batch correction using ComBat you need to select non-parametric correction if the distribution isn't normal, because the regular parametric method assumes a normal distribution. I also know you're supposed to run DE on the raw counts without corrections so I can't use the batch corrected data. What I do not deeply understand is how DE programs subtract out the covariates and if they need a normally distributed dataset to do so.
So my question is: Can I run EdgeR or DESeq2 with batch as covariate the way I normally do? Or will the bimodality cause issues?