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Table 1 Validation of four differential gene expression analysis methods for RNA-Seq

From: Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq

Parametersa edgeR Cuffdiff2 TSPM DESeq2
Total number of identified DEGsb 82 136 8 1
Number for DEGs selected for qPCR validation 51 79 8 1
Sensitivity (True positivity rate) (%) 76.67 51.67 5.00 1.67
Specificity (True negativity rate) (%) 90.91 12.73 90.91 100.00
False positivity rate (%) 9.09 87.27 9.09 0.00
False negativity rate (%) 23.33 48.33 95.00 98.33
Positive predictive value (%) 90.20 39.24 37.50 100.00
Negative predictive value (%) 78.13 19.44 46.73 48.25
Positive likelihood ratio 8.43 0.59 0.55
Negative Likelihood ratio 0.26 3.80 1.05 0.98
Overall agreement (%) 83.48 33.04 46.09 48.70
  1. aReplication of differential expression by quantitative Polymerase Chain Reaction (qPCR) was the reference standard
  2. bDifferentially Expressed Genes, after Benjamini-Hochberg false discovery correction at 5 %; TSPM: Two-stage Poisson Model