Computational protocol: Human papillomavirus genotype and viral load agreement between paired first-void urine and clinician-collected cervical samples

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Protocol publication

[…] The percent correct and Cohen’s Kappa (κ) were calculated to assess the HPV genotype agreement between paired samples. In addition, the McNemar’s odds ratio (OR) and test were computed to compare the association between FVU or CS for a given HPV genotype. In case a zero cell count occurred, a constant of 1 was added to each cell in the table []. The Wilcoxon matched pairs signed rank test was used to test for differences in dependent continuous measures and for differences within levels of categorical measures. hDNA and HPV copy number correlations were calculated using Pearson and Spearman rank correlations, respectively. All p-values were corrected for multiple testing using the false discovery rate (FDR) method []. Statistical analyses were performed at a significance level of 5% using the statistical software R version 3.3.3 [] and IBM SPSS Statistics Version 24. Additional graphs were generated using Excel Microsoft Office Professional Plus 2016 and JMP Pro 13. […]

Pipeline specifications

Software tools SPSS, JMP Pro
Application Miscellaneous
Organisms Human papillomavirus, Homo sapiens, Human papillomavirus type 16, Human papillomavirus type 18