Normalization after merging Seurat objects

Question

[Maria17]

Hi All,

I'm working on single-cell RNA seq data with the Seurat package. I made 3 Seurat objects and normalized them. now I want to merge 3 Seurats . after merging should I do the normalization step again? in normal workflow in Seurat Integration here only mentioned ScaleData .in case of second-time normalization what happens?

Any recommendation would be appreciated. Thanks.

Maria

Answer 1

[fracarb8]

You don't need to normalise your data after merging, because LogNormalize only log transform your data on a sample level, and each sample is treated independently. The values won't change after merging. On the other hand, you need to re-scale your data because the scaling transformation takes into account the content (samples) of your dataset. The values will be different after merging.