Table 1.

Computed relative mRNA proportions. Computed relative mRNA proportions p_M (macrophages) and p_F (fibroblasts) for patients 1–6 calculated for different chip evaluation methods. The proportion of non-adherent cells is p_N = 1 - p_M - p_F. The primed 1 in 'patient 1' (RA)' indicates the use of the second tissue chip replicate for patient 1. Additional stepwise local regression normalization is indicated by lr. The proportions are given in percent. Probe set summaries: MAS-S: Microarray Suite 5.0 signal algorithm, RMA: Robust Multiarray Analysis, MBEI: Model Based Expression Index, GP: GenePublisher (not available for HG-U95A chips, patient 1), the R implementation of MBEI was used with the same settings as in GP. Normalization methods: t: trimmed mean, clr: cyclic local regression, q: quantile normalization, c: centralization.

chip evaluation method	patient 1' (RA)				patient 2 (RA)				patient 3 (RA)				patient 4 (QA)				patient 5 (QA)				patient 6 (QA)
			lr				lr				lr				lr				lr				lr
	M	F	M	F	M	F	M	F	M	F	M	F	M	F	M	F	M	F	M	F	M	F	M	F
MAS-S t	29	16	29	19	82	9	79	6	64	27	64	29	57	24	57	27	72	21	69	20	86	13	81	19
MAS-S t clr	32	18	29	22	90	10	86	5	66	30	64	33	65	25	64	30	74	21	68	25	78	22	74	26
MAS-S t q	31	14	24	22	92	8	93	6	69	30	63	34	66	23	63	30	87	07	71	22	71	29	67	33
MAS-S t c	31	15	29	17	80	5	80	6	59	31	65	30	71	16	66	21	80	13	80	11	96	2	80	20
RMA	44	24	28	31	95	5	82	16	49	42	45	45	60	26	46	36	94	0	85	8	96	0	100	0
MBEI	44	15	42	19	91	5	76	2	38	52	45	49	66	2	57	10	98	0	92	5	100	0	99	1
MBEI-GP	--	--	--	--	98	1	88	9	26	62	43	55	57	5	38	18	92	0	94	0	100	0	100	0