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Table 3 Cluster-based prediction of phenotypic resistance relative to controls.

From: A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

With all data   RTV NFV ATV APV IDV LPV SQV TPV DRV
CTL1 (Random) % correct 35 36 29 21 22 26 29 31 29
CTL1 (Random) RMSE 1.34 1.13 1.21 1.2 1.05 1.01 1.26 0.98 0.76
CTL2 (Average) % correct 46 43 62 60 62 56 57 47 34
CTL2 (Average) RMSE 0.60 0.54 0.36 0.34 0.26 0.28 0.41 0.67 0.67
Cluster-based % correct 81 75 74 70 63 67 65 50 67
Cluster-based RMSE 0.35 0.34 0.38 0.33 0.29 0.25 0.50 0.71 0.29
Without nonresistant clusters   RTV NFV ATV APV IDV LPV SQV TPV DRV
CTL1 (Random) % correct 78 66 45 27 22 29 34 18 29
CTL1 (Random) RMSE 0.54 0.68 0.84 0.97 0.86 0.83 1.06 1.00 0.74
CTL2 (Average) % correct 28 32 49 51 52 43 46 28 11
CTL2 (Average) RMSE 0.74 0.64 0.45 0.41 0.32 0.34 0.51 0.84 0.84
Cluster-based % correct 89 82 73 62 55 58 60 34 56
Cluster-based RMSE 0.26 0.23 0.38 0.40 0.36 0.31 0.62 0.89 0.36
  1. Percent of viruses whose resistance score toward each drug was correctly classified ("% correct"), as well as the RMS error (in scaled resistance units) over all sequences of the phenotypic difference between predicted and actual phenotype ("RMSE") using the two controls described in the text ("CTL1 (Random)" and "CTL2 (Average)" and the cluster-based prediction. The top panel presents results using all 398 sequences, and the bottom panel shows results after removing the two clusters showing little or no phenotypic resistance to any drug.