Normalization after merging Seurat objects
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2.8 years ago
Maria17 ▴ 40

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

Seq Seurat ScRNA-Seq RNA • 2.9k views
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Entering edit mode
2.8 years ago
fracarb8 ★ 1.6k

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.

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