The SNPs were analyzed for allele frequency differences between the cases and controls in each population sample using logistic regression.
The polygenic score was tested for ability to predict SA or TWOSI/TESI in the validation sample using logistic regression, with principal components as required, to calculate Nagelkerke's pseudo-R, a measure of the variance explained [Nagelkerke, 1991].
As independent validation, we repeated the analyses in the test set no. 2 (Lagarde's 60 sample series) using logistic regression.
The joint analysis of all combined samples was performed using logistic regression with gender, age and sample cohorts as covariates.
In the matched sample analysis, comparisons of adherence among samples were conducted using logistic regression with adherence as a dichotomous outcome.
Case and control samples were analysed using logistic regression, adjusting for 12 broad geographical regions within Great Britain (southwestern, southern, southeastern, London, eastern, Wales, Midlands, North Midlands, northwestern, East and West Riding, northern and Scotland) to exclude the possibility of confounding by geography.
However, suggestive genotypic association findings in the Swedish sample were verified using logistic regression with the gender as a covariate, and displayed a very minor gender effect.
To investigate the potential that there may be differences in resistance prevalences among NTSEC recovered from individual fecal samples when compared to those recovered from composite (pen-floor) samples, isolates recovered from these two sample types were compared using logistic regression.
DOI: http://dx.doi.org/10.7554/eLife.011230074 3007 genome-wide analyses of associations between human SNPs and HIV-1 amino acid variants were performed in the full sample of 1071 individuals using logistic regression corrected for viral phylogeny (Carlson et al., 2008; Carlson et al., 2012).
Data on putative risk factors were collected at the time of sampling and analyzed for association using logistic regression.
