Student's t test^{a} | Unmoderated t test^{b} | Moderated t test^{c} | |||||||
---|---|---|---|---|---|---|---|---|---|

p^{d} | Bonf^{e} | FDR^{f} | p | Bonf | FDR | p | Bonf | FDR | |

N^{g} | 954 | 954 | 954 | 830 | 830 | 830 | 1,172 | 1,172 | 1,172 |

<0.05^{h} | 325 | 56 | 272 | 144 | 14 | 58 | 214 | 11 | 45 |

E(FP)^{i} | 48 | 0.05 | 14 | 42 | 0.05 | 3 | 59 | 0.05 | 2 |

FDR (%)^{j} | 15 | 0.1 | 5 | 29 | 0.4 | 5 | 28 | 0.5 | 5 |

↵

^{a}Student's*t*test where each protein abundance measurement was treated as independent using a simple linear model accounting for^{14}N and^{15}N label reversal only.↵

^{b}Unmoderated*t*test with the full linear model.↵

^{c}Empirical Bayes moderated*t*test with the full linear model.↵

^{d}*p*, the number of differentially abundant proteins with statistic <0.05 for unadjusted*p*values.↵

^{e}Bonf, the number of differentially abundant proteins with statistic <0.05 for Bonferroni method-corrected*p*values.↵

^{f}FDR, the number of differentially abundant proteins with statistic <0.05 for FDR-corrected*q*values.↵

^{g}The number of proteins analyzed from the 1,172 quantified proteins; proteins analyzed by the Student's*t*test had at least two observations, the unmoderated*t*test had at least three observations or two observations from the same extraction buffer, and the moderated*t*test had at least one observation.↵

^{h}Number of differentially abundant proteins with statistic <0.05.↵

^{i}Expected false positives.↵

^{j}FDR was calculated by dividing E(FP) by the number of differentially abundant proteins with statistic <0.05.