The goal of fold change (FC) analysis is to compare the absolute value of change between two group means. Since column-wise normalization (i.e. log transformation and various scaling) will significantly change absolute values, FC calculation are using data **before** column-wise normalization was applied (i.e. at original scale). The significant features are those features whose FCs are beyond the given FC threshold (either up or down).

- For unpaired analysis, FCs are calculated as the ratios between two
**group means (M1/M2)**. - For paired analysis, FCs are calculated by computing the ratio between paired samples, (i.e. one FC per pair), and then compute their means (i.e.
**pair means**).