9.6.1 Preprocessing step 2 : Expression normalization
After removing unwanted genes 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 gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result. There have been many methods to normalize the data, but this is the simplest and the most intuitive. The division by total expression is done to change all expression counts to a relative measure, since experience has suggested that technical factors (e.g. capture rate, efficiency of reverse transcription) are largely responsible for the variation in the number of molecules per cell, although genuine biological factors (e.g. cell cycle stage, cell size) also play a smaller, but non-negligible role. The log-transformation is a commonly used transformation that has many desirable properties, such as variance stabilization (can you think of others?).