IS there any way to adjust TPM(data slot) matrix by integration?

[vanqilei]

Thanks for ur attention,there are some analysis in my workflow that need the log(TPM+1) form,like the heatmap of expression levels, comparative trajactories among developmental stages on specific genes, using clusterGV or GSVA etc. I wanna use these integration ideas in Seurat but a single dimensional reduction is not enough.
And by the way,how can we deal with batch effect when perform differential analysis with two type of cells(even maybe same type but different species) that from 2 batches,it seems that batch effect align with biological condition can not be handeled.And I dont know if there is any setting about batch in Seurat when using Findmarkers.