TABLE 1

A 2 × 2 contingency table of (unreplicated) digital gene expression (DGE) measures for testing differential expression between Treatment1 and Treatment2 of gene A

Treatment1Treatment2Total
Gene AEmbedded ImageEmbedded ImageEmbedded Image
Remaining genesEmbedded ImageEmbedded ImageEmbedded Image
TotalEmbedded ImageEmbedded ImageEmbedded Image
  • The cell counts Embedded Image represent the DGE count for gene A (k = 1) or the remaining genes (k = 2) for Treatmenti, I = 1, 2. The Embedded Image marginal row total is denoted Embedded Image, Embedded Image is the marginal total for column i, and Embedded Image is the grand total.