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Table 2 comparison between RMA and tRMA in the affycomp benchmark

From: Algorithm-driven Artifacts in median polish summarization of Microarray data

  MAS5 RMA tRMA Best possible
Signal detect slope 0.71 0.63 0.63 1
Signal detect R2 0.86 0.80 0.80 1
Obs-intended-fc slope 0.69 0.61 0.61 1
Obs-(low)int-fc slope 0.65 0.36 0.36 1
null log-fc IQR 0.85 0.19 0.20 0
null log-fc 99.9% 4.48 0.57 0.58 0
low AUC 0.07 0.40 0.39 1
med AUC 0.00 0.87 0.86 1
high AUC 0.00 0.46 0.44 1
weighted avg AUC 0.05 0.52 0.51 1
Median SD 0.63 0.11 0.12 0
low.slope 0.72 0.35 0.35 1
med.slope 0.80 0.76 0.76 1
high.slope 0.45 0.47 0.47 1
  1. affycompII most indicative results (as in [6]) for MAS5, RMA and tRMA, spike-in HGU95 dataset. Differences between RMA and tRMA are trivial, especially when compared to other methods (see also [6]).