Differential expression using Scran batch corrected data

Question

[baldissera152]

Hi, guys

I intend to to integrate two single-cell RNA-Seq datasets and then correct their expression values for batch effect using Scran mnnCorrect function. However, after mnn correction, the output is a matrix which includes logtransformed and negative values. Since softwares usually require raw count data for differential expression (Deseq2 for example) I am looking for a way to perform the analysis after the integration and correction for batch effect.

Do you have any kind of suggestion or guidelines on how could I proceed?

Thanks in advance!