Table 1

Scaling and capping of raw fold-change values.

Drug

Base

Max

Min


RTV

2.5

7.30

-1.76


NFV

3.6

4.99

-0.94


ATV

5.2**

3.97

-0.73


APV

6.6*

3.17

-0.85


IDV

10**

2.70

-0.52


LPV

22.3*

2.00

-0.52


SQV

5.3*

4.16

-0.97


TPV

4.0*

4.82

-1.16


DRV

30.0*

1.83*

-0.47*


The bases used for log scaling each drug were informed by Monogram biological and clinical cutoffs as described in the text. Unstarred bases are equal to the available Monogram biological cutoffs; singly-starred bases were calculated as the geometric mean of lower and upper clinical cutoffs. Double-starred bases are equal to the single available Monogram clinical cutoff. For all drugs, scaled values were capped to the least extreme minima and maxima (those of DRV, shown in bold and starred). Maxima in the table were generally used when assay upper limits had been reached, representing that the actual fold resistance was higher than the assay could accurately determine. The maximum measurable fold-change can vary for a given drug between isolates, but due to the cap being well below their ranges of maximum fold-change values, our results are entirely unaffected by variation for most drugs; the upper fold-change limits for DRV and LPV may have at times been slightly lower than the upper cap used here, but as a check for robustness, preliminary results were generated with varying upper caps and were qualitatively similar to those shown here.

Doherty et al. BMC Bioinformatics 2011 12:477   doi:10.1186/1471-2105-12-477

Open Data