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Table 1 Synthetic example to illustrate the effect of addition of pseudo-counts over the estimation of LFCs in overall expression

From: Beyond comparisons of means: understanding changes in gene expression at the single-cell level

  Empirical Adding 0.5 Adding 1
  estimate pseudo-counts pseudo-count
Overall expression rate in population 1 (\(\mu ^{(1)}_{i}\)) 10 10.5 11
Overall expression rate in population 2 (\(\mu ^{(2)}_{i}\)) 0 0.5 1
LFC in overall expression 1 vs 2 + 3.04 2.40
  1. For simplicity, we assume that normalization is not required so that pseudo-counts are linearly reflected in the overall expression rates. While pseudo-counts introduce an additive effect, LFC estimates measure changes on a multiplicative scale. Hence, addition of pseudo-counts leads to an artificial deflation of LFC estimates. As a consequence, such estimates cannot be meaningfully interpreted