Table 1 Definition of true and false-positive genes (TPi and FPi) and of true and false-negative genes (TNi and FNi) at a certain level of rejection α=pi (P-value of the ith gene after ranking them in ascending order by P-value) (for each of them, the formula of the expected value is given)

From: Balancing false positives and false negatives for the detection of differential expression in malignancies

 

Actually differentially expressed?

 

Declared differentially expressed?

Yes

No

 

Yes (P⩽pi)

TPi≈ i−pi N0

FPi≈pi N0 (Type I error)

Posi=i

No (P>pi)

FNi≈ N1−i+pi N0 (Type II error)

TNi≈(1−pi)N0

Negi=N−i

 

N 1

N 0

 
  1. N=total number of genes; N0=number of genes without actual differential expression; N1=number of genes with actual differential expression (N=N0+N1); Posi=number of genes declared positive or differentially expressed at rejection level pi; Negi=number of genes declared negative at rejection level pi.
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