Table 1. Number of differentially expressed genes for the comparison between ADT and CRM.

	FC	APV	cohort A	FC	APV	cohort B	FC	APV	cohort C
cuffdiff2	2	0.05	35	2	0.05	26	2	0.05	63
deseq2	1.3	0.10*	1	1.4	0.05	6	1.3	0.10*	3
EBSeq	2	0.05	1	2	0.05	11	2	0.05	71
edgeR	2	0.05	2	2	0.05	31	2	0.05	4
voom	2	0.05*	8	2	0.05*	11	2	0.05*	19
voom+weight	2	0.05*	17	2	0.05*	11	2	0.05*	14

FC: fold change, APV: adjusted p-value, *p-value is used for cutoff.