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Table 1 Number of differentially expressed genes using several cut-off strategies

From: Gene expression variation between mouse inbred strains

  Between strains Within strains
  MA-ANOVA Hierarchical t-test
   CBA BL10 BL6 DBA BALB
Correlation   0.95 0.95 0.87 0.87 0.92
Naive (p < 0.05) 718 737 610 963 1043 483
Bonferroni 0 2 4 1 0 3
FDR 10% 88 2 4 14 0 16
  1. Correlation between two individuals per strain was calculated using Pearson's correlation coefficient. Significance levels (p-values) between strains were calculated with MA-ANOVA, and within strains using the hierarchical t-test. Differential gene expression was determined by selecting genes with p-values lower than a specified threshold. Thresholds were selected using three different strategies; naive, Bonferroni corrected, and False Discovery Rate (10%), and resulted in different numbers of significantly differentially expressed genes.