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?