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Table 2 Generating Reference Standards with r-DEG methods in datasets with replicates Standards

From: Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine

Method Yeast (n = 30 paired samples), genome size = 7126 genes MCF7 (n = 4 paired samples), genome size = ~ 22,000 genes
FDR Threshold Number of DEGs Percent of Genome as DEG FDR Threshold Number of DEGs Percent of Genome as DEG
edgeR .05 4437 62% .005 3231 14%
DESeq .05 4594 64% .001 3207 14%
DESeq2 .05 4802 67% .0005 3255 15%
DEGseq .05 5087 71% 3.56e-12 3351 15%
NOISeq .05 3914 55% 0.078 3397 15%
Intersection of all methods n/a 3118 44% n/a 1173 5%
Union of all methods n/a 6425 90% n/a 6039 27%
  1. FDRs are adjusted to obtain lists of DEGs of the same length as reported in the original publications. As shown with the intersection of all DEGs predicted by distinct methods, determining a gold standard in RNA-Seq analyses of multiple biological isogenic replicates remains a challenge
  2. n/a not applicable