What's the difference between "fold change" and "paired fold change" analyses?

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 ).