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Table 1 Results of affycomp comparative benchmark.

From: A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

Metric Optimal Value Full refRMA Classic RMA MAS 5.0 MAS 5.0+32
Null log-fc IQR 0.00 0.20 0.13 0.47 0.34
Null log-fc 99% 0.00 0.51 0.29 2.83 1.30
Null log-fc 99.9% 0.00 0.74 0.40 4.01 1.81
Low AUC 1.00 0.20 0.45 0.00 0.03
Med AUC 1.00 0.53 0.87 0.00 0.01
High AUC 1.00 0.67 0.92 0.00 0.01
Weighted Avg AUC 1.00 0.28 0.55 0.00 0.03
Low slope 1.00 0.27 0.25 0.61 0.42
Med slope 1.00 0.68 0.69 0.70 0.67
High slope 1.00 0.87 0.82 0.81 0.81
  1. Specific descriptions of each metric are provided in the original publication describing the affycomp system [9].