Question regarding normalization in Seurat

Question

[ylin575]

Hello everyone,

I have a question regarding Seurat regarding data normalization. I am following the tutorial on the pbmc3k dataset. After removing unwanted cells, the next step is to normalize data. The tutorial has this to say:

After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result. Normalized values are stored in pbmc[["RNA"]]@data.

My question is what is this 'total expression', is it the total expression (i.e. total RNA molecule count) in the cell or the total expression in the entire dataset?

Thank you!

Yong

Answer 1

[ATpoint]

It is the sum of counts for that cell, so basically if a given cell has a given column in the count matrix it is the colSum of that column.

[ylin575]

Thanks for the clarification!