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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.

From: Robust computational reconstitution – a new method for the comparative analysis of gene expression in tissues and isolated cell fractions

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