Identification and characterization of genes with absolute mRNA abundances changes in tumor cells with varied transcriptome sizes

Table 3 Simulation evaluation with different FC levels for edgeR and RankCompV2

FC level	Factor	edgeR				RankCompV2
FC level	Factor	Sen	Spe	F-score	FDR	Sen	Spe	F-score	FDR
1.5	0.9360	85.83%	100.00%	92.37%	0.00%	56.10%	100.00%	71.88%	0.00%
2	0.8647	98.76%	99.76%	99.26%	0.51%	82.50%	100.00%	90.41%	0.00%
2.5	0.7996	99.52%	97.82%	98.63%	4.23%	93.50%	100.00%	96.64%	0.00%
3	0.7448	99.78%	94.85%	97.21%	9.83%	97.79%	100.00%	98.88%	0.01%
3.5	0.6965	99.88%	92.61%	96.08%	13.87%	98.84%	99.98%	99.40%	0.05%

Note: FC is the abbreviation of Fold change; Factor is defined as the fold change of the transcriptome sizes between the simulated tumor cell and the normal cell; Sen represents sensitivity defined as the ratio of correctly identified DEGs to all true DEGs; Spe represents specificity defined as the ratio of correctly identified non-DEGs to all true non-DEGs); F-score is a harmonic mean of the sensitivity and the specificity; FDR is the abbreviation of false discovery rate defined as the ratio of true non-DEGs to all identified DEGs

ISSN: 1471-2164