Table 3.

Differential expression

		Ovarian cancer			Gaucher
		CM10	Q10	CM10/Q10
label	Ciphergen A	43	19	57	57
	Ciphergen B	37	15	47	46
	Ciphergen C	41	13	50	30
chip	Ciphergen A	6	57	69	8
	Ciphergen B	10	35	52	7
	Ciphergen C	0	15	16	10
label:chip	Ciphergen A	0	0	0	3
	Ciphergen B	0	0	0	0
	Ciphergen C	0	0	0	0
label	Cromwell A	153	17	142	43
	Cromwell B	112	12	95	40
	Cromwell C	67	8	61	29
chip	Cromwell A	0	0	0	22
	Cromwell B	0	0	0	37
	Cromwell C	0	0	0	26
label:chip	Cromwell A	0	0	0	1
	Cromwell B	0	0	0	0
	Cromwell C	0	0	0	0

Number of peaks with an adjusted p-value < 0,2 (ANOVA and correction for multiple testing) for different peak detection settings (A-C for both Ciphergen and Cromwell) for CM10, Q10, and CM10/Q10 (ovarian cancer dataset) and the Gaucher dataset. An ANOVA was performed for label effect (patient versus control), chip (array) effect and interaction effect label:chip.