5.1 Normalization

In order to normalize the data we recommend using variance stabilized transformation available in the SCTransform function in Seurat as of v3.0.

Since we have a known batch effect between the two sections, we will try to deal with that by specifying the batch in the vars.to.regress argument of the function. With more severe batch effects, you may need to integrate the two sections using a data integration method.

Let’s see the effect of batch correction.

se.norm <- SCTransform(se.subset)
se.cor <- SCTransform(se.subset, vars.to.regress = "batch")