Comparison of the Precision and Sensitivity of
the Antivirogram and PhenoSense HIV Drug Susceptibility Assays

1. raw data sets
2. statistical analyses
   1. Parametric and Nonparametric Measures of Reproducibility of Susceptibility Tests
      Performed on HIV-1 Isolates Lacking Drug-Resistance Mutations.
   2. Parametric and Nonparametric Measures of Reproducibility of Susceptibility Tests
      Performed on HIV-1 Isolates eith Matching Patterns of Drug-Resistance Mutations.
   3. Drug Resistance Prediction Using Biological Cut-offs for the Most Common Patterns of NRTI Resistance Mutations.
   4. ROC (Receiver Operator Characteristic) curves showing the Sensitivity and Specificity in Detecting Resistance
      to ABC(abacavir), DDI(didanosine) and D4T(stabudine) of Isolates containing M41L+M184V+T215Y+/-L210W.

raw data sets

• Antivirogram (Virco)
  protease inhibitor susceptibilities: vircoRAWdata_PI.txt,    RT inhibitor susceptibilities: vircoRAWdata_RT.txt
• PhenoSense (Virologic)
  protease inhibitor susceptibilities: virologicRAWdata_PI.txt,    RT inhibitor susceptibilities: virologicRAWdata_RT.txt
  description of files
  references -- where the isolates and susceptibilities came from

statistical analyses

Each statistical analysis uses a perl script to transform raw data and generate input data for a R script.
Each R script does a statistical testing on the transformed data.

1. Parametric and Nonparametric Measures of Reproducibility of Susceptibility Tests
   Performed on HIV-1 Isolates Lacking Drug-Resistance Mutations. [Table 1]
   • script for raw data transformation: gettable1data.pl
     input: raw data files
     output (description) : vircotable1PI.txt / virologictable1PI.txt / vircotable1RT.txt / virologictable1RT.txt
   • statistical test: analysis_table1.R
     input: vircotable1PI.txt / virologictable1PI.txt / vircotable1RT.txt / virologictable1RT.txt
     output: [Table 1]
   • Distribution of median absolute deviation from the median of the log-transformed levels of fold-resistance: [supplementary figure]

2. Parametric and Nonparametric Measures of Reproducibility of Susceptibility Tests
   Performed on HIV-1 Isolates with Matching Patterns of Drug-Resistance Mutations. [Table 2]
   • script for raw data transformation: gettable2data.pl
     input: raw data files
     output (description) : vircotable2PI.txt / virologictable2PI.txt / vircotable2RT.txt / virologictable2RT.txt
   • statistical test: analysis_table2.R
     input: vircotable2PI.txt / virologictable2PI.txt / vircotable2RT.txt / virologictable2RT.txt
     output: [Table 2]
   • Distribution of median absolute deviation from the median of the log-transformed levels of fold-resistance: [supplementary figure]

3. Drug Resistance Prediction Using Biological Cut-offs for the Most Common Patterns of NRTI Resistance Mutations. [Table 3]
   • script for raw data transformation: gettable3data.pl
     input: raw data files
     output (description) : vircotable3data.txt / virologictable3data.txt
   • statistical test: analysis_table3.R
     input: vircotable3data.txt / virologictable3data.txt
     output: [Table 3]

4. ROC (Receiver Operator Characteristic) curves showing the Sensitivity and Specificity in Detecting Resistance
   to ABC(abacavir), DDI(didanosine) and D4T(stabudine) of Isolates containing M41L+M184V+T215Y+/-L210W. [Figure 1]
   • statistical test: plotROC.R & library of R scripts
     input : vircotable1RT.txt / virologictable1RT.txt/ vircotable2RT.txt / virologictable2RT.txt
     output: [Figure 1]