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

BMC Medical Genomics

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

Method	Yeast (n = 30 paired samples), genome size = 7126 genes			MCF7 (n = 4 paired samples), genome size = ~ 22,000 genes
Method	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%

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
n/a not applicable

ISSN: 1755-8794