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Table 2 Sample size and anticipated average power calculated by our method and observed average power by the voom and limma pipeline while controlling FDR using q-value procedure based on parameters at different m for three simulation settings

From: Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments

 

Simulation 1

Simulation 2

Simulation 3

 

Our Method

Our Method

RnaSeqSampleSize

Our Method

m

Sample

Anticipated

Observed

Sample

Anticipated

Observed

Sample

Estimated

Sample

Anticipated

Observed

 

size

power

power

size

power

power

size

power

size

power

power

50

35

0.802

0.858

13

0.810

0.876

9

0.780

22

0.800

0.801

100

34

0.814

0.846

13

0.814

0.876

9

0.724

22

0.803

0.801

200

34

0.815

0.846

13

0.823

0.876

9

0.765

22

0.804

0.801

500

33

0.817

0.833

13

0.827

0.876

9

0.769

22

0.805

0.801

1000

32

0.800

0.804

13

0.826

0.876

9

0.764

22

0.805

0.801

  1. We also present the comparison between our method and RnaSeqSampleSize R package for simulation 2, where the right two columns are sample size and power calculated by the RnaSeqSampleSize R package