Fold change rank ordering statistics: a new method for detecting differentially expressed genes

BMC Bioinformatics

Table 2 Comparative results for the Platinum spike dataset

Status	A vs B	Number	FCROS	FC	WAD	RP	Ttest	SAM	TREAT
EE	0	13337	216	220	19	221	142	203	176
DE	0.25	192	161	161	158	161	162	161	161
DE	0.28	174	162	163	154	163	157	163	163
DE	0.4	163	132	134	127	133	131	133	133
DE	0.66	189	151	155	147	154	89	149	139
DE	0.83	166	46	43	111	40	118	60	83
EE	1	3426	52	49	232	50	158	56	77
DE	1.5	167	134	134	131	135	114	135	131
DE	1.7	166	150	150	141	150	145	149	149
DE	2	184	161	161	158	162	162	162	161
DE	3	98	94	94	92	94	94	94	94
DE	3.5	445	397	394	382	396	388	393	392
EE/DE	MC	231	74	74	77	73	71	74	73
EE/DE	MF	14	10	8	11	8	9	8	8
True DE genes detected			1588	1589	1601	1588	1560	1599	1606
Error			18.14%	18.09%	17.47%	18.14%	19.58%	17.57%	17.21%
AUC			0.91054	0.90984	0.92030	0.91077	0.90891	0.91084	0.91094

Platinum Spike dataset: number of genes detected by each method for a given change condition. EE and DE are for equally expressed and differentially expressed, respectively. "A vs B" is the designated fold change and "Number" is the number of probes for each change condition. Detection error and the AUC are also given at the bottom of the Table.

ISSN: 1471-2105