Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis

Table 2 Percentage of genes identical among all genes detected by different combinations of normalization and statistical analysis

	Invariant feature; AD, F	Invariant feature; AD, KW	Invariant feature; AD, SAM	Invariant feature; MBEV, F	Invariant feature; MBEV, KW	Invariant feature; MBEV, SAM	Invariant set; F	Invariant set; KW	Invariant set; SAM	Global scaling; F	Global scaling; KW	Global scaling; SAM
Invariant feature; AD, F		93	100	78	83	92	81	83	88	64	74	78
Invariant feature; AD, KW	74		95	67	79	82	74	79	81	55	67	69
Invariant feature; AD, SAM	56	66		51	59	74	58	61	66	41	50	54
Invariant feature; MBEV, F	69	75	82		96	100	77	80	82	58	67	70
Invariant feature; MBEV, KW	62	74	79	80		95	71	75	77	51	62	64
Invariant feature; MBEV, SAM	56	63	81	68	77		63	66	70	44	53	57
Invariant set; F	59	69	77	63	70	76		98	100	56	67	70
Invariant set; KW	56	67	74	60	68	74	90		96	52	66	66
Invariant set; SAM	55	64	74	58	65	73	85	89		49	61	66
Global scaling; F	80	87	92	81	86	90	95^*	96^*	98^*		100	100
Global scaling; KW	72	83	88	73	82	85	89	96^*	95^*	78		93
Global scaling; SAM	70	78	88	71	77	84	85	89	94^*	72	86

Percentages are relative to the method defined in the column headings. Values of 100% and greater than 90% are highlighted in bold. ^*Percentage of genes identified after invariant probe set normalization that are also identified after global scaling (see text for details).