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All survival models were checked for proportionality.
The final Cox models were checked for proportionality assumption based on the Schoenfeld residuals and were stratified by sex and/or initial disease type to hold the proportionality assumption.
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In order to confirm that the linear range of the instruments also corresponded to the dynamic range of signal output, the 10-fold differences in copy number between samples were compared with signal output to check for proportionality.
In models (2), (4) and (7), hazard proportionality was checked for each explicative variable by plotting log-minus-log survival curves obtained by the Kaplan and Meier estimator [ 23] and by testing the scaled Schoenfeld residuals [ 24] separately in the reference and relative samples.
The proportionality assumption was checked for each of the variables under study with scaled Schoenfeld residuals and by the proportionality test [ 25- 27].
To assess the proportionality assumption, we checked for interaction between each risk factor and time since AIDS diagnosis; for highly active antiretroviral therapy, a time-dependent covariate, we assessed interaction with time since start of treatment.
Proportionality of odds across the HAQ groups was checked for each regression.
We checked for possible deviation from the proportional hazards assumption of the Cox regression model by using the non-proportionality test on the basis of the Schoenfeldt residuals.
We checked the proportionality assumption with the log-log plots.
We checked the proportionality of hazard over time using Schoenfeld's residuals [ 28].
Check, check, check for Ms. Sandberg.
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