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Table 2 Statistical analysis of DEGs from four normalization and test statistics given a nominal FDR ≤ 0.05. Listed are the number of TP and FP genes, the observed FDR and the PPV, sensitivity and specificity using MAQC datasets

From: Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

DataStatistical test (package)Methods# of TP# of FPPPVActual FDRSensitivitySpecificity
MAQC2 (n = 2)Exact test (edgeR)UQ-pgQ2377220.9450.0550.9670.851
TMM384810.8260.1740.9850.453
RLE380910.8070.1930.9740.385
UQ379920.8050.1950.9720.378
Wald test (DESeq2)UQ-pgQ2385490.8870.1130.9870.669
UQ374800.8240.1760.9590.460
TMM374820.8200.1800.9590.446
RLE376830.8190.1810.9640.439
T-test (voom-limma)UQ-pgQ2 & UQ363760.8270.1730.9310.487
TMM373970.7940.2060.9560.345
RLE364920.7980.2020.9330.378
QL F-test (edgeR)UQ-pgQ2387590.8680.1320.9970.587
TMM3851030.7890.2110.9920.280
RLE & UQ3851080.7810.2190.9920.245
MAQC3 (n = 5)Exact test (edgeR)UQ-pgQ2383510.8820.1180.9870.643
TMM386930.8060.1940.9950.350
RLE386980.7980.2020.9950.315
UQ386980.7980.2020.9950.315
Wald test (DESeq2)UQ-pgQ2384830.8220.1780.9900.420
UQ3871010.7930.2070.9970.294
TMM3861030.7890.2110.9950.280
RLE3851020.7910.2090.9920.287
T-test (voom-limma)UQ-pgQ2 & UQ362580.8620.1380.9320.594
RLE376640.8560.1460.9690.552
TMM350600.8530.1460.9020.580
QL F-test (edgeR)UQ-pgQ2382850.8180.1820.9850.406
TMM385990.7960.2050.9920.308
RLE3861050.7860.2140.9950.267
UQ3861040.7880.2120.9950.273