The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison

BMC Bioinformatics

Table 2 Retention counts and percentages. Retention counts (RC) and retention percentages (RP) for the differentially expressed gene sets of Table 1. RC is the number of genes in a set before the MIDAS step that remain in the set after that step. RC is the number of genes in the set before the MIDAS step that remain in the set after that step. RP is the percentage of remaining genes with respect to the number of genes in the set after the MIDAS step. RC and RP are reported for the intersections IIV_∩ IIV_T, IIV_T ∩ IIV_TL, IIV_TL ∩ IIV_TLS, and IIV_TLS ∩ IIV_TLSF, as well as intersection IIV_∩ ∩IIV_TLSF, which corresponds to the effect of MIDAS steps from the start of the pipeline to the end. The ALL entries correspond to the H1 hypotheses of the GOT model (see Materials and Methods).

		IIV ∩		IIV_T∩		IIV_TL∩		IIV_TLS∩		IIV ∩
		IIV_T		IIV_TL		IIV_TLS		IIV_TLSF		IIV_TLSF
Genotype		RC	RP	RC	RP	RC	RP	RC	RP	RC	RP
		GP Model — Experiment 1
WT	+	545	95.45	74	15.20	285	57.58	456	99.13	59	12.83
WT	-	532	96.20	55	11.02	306	61.32	459	99.78	53	11.52
antiPLD	+	403	95.72	58	13.18	278	59.02	430	99.77	46	10.67
antiPLD	-	326	94.22	45	11.81	203	55.92	330	98.80	33	9.88
		GOT Model — Experiment 2
Col-0	+	224	72.49	221	91.32	219	91.25	172	63.70	159	58.89
Col-0	-	121	70.76	150	84.27	165	91.67	120	65.57	92	50.27
Cvi-0	+	81	75.00	65	79.27	71	91.25	49	69.01	36	50.70
Cvi-0	-	60	64.52	60	81.08	63	88.73	41	61.19	38	56.72
ws	+	223	64.45	230	82.44	248	92.19	108	72.00	101	67.33
ws	-	293	84.44	267	78.53	314	92.35	180	80.36	149	66.52
Th	+	236	59.30	308	88.00	330	90.91	256	70.91	201	55.68
Th	-	183	74.69	210	87.14	225	91.46	172	71.67	144	60.00
ALL	+	282	65.89	307	85.99	333	94.07	200	68.97	177	61.03
ALL	-	196	75.10	196	77.47	230	92.74	133	68.21	103	52.82

ISSN: 1471-2105