Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Statistical analysis

JM Jacob A. Miller
MS Malaya K. Sahoo
FY Fumiko Yamamoto
CH ChunHong Huang
HW Hannah Wang
JZ James L. Zehnder
QL Quynh-Thu Le
BP Benjamin A. Pinsky
request Request a Protocol
ask Ask a question
Favorite

Positive percent agreement (PPA) and negative percent agreement (NPA) were reported with Clopper-Pearson score 95% binomial confidence intervals using NGS as the reference method. The 95% LLOD was calculated using probit regression for each target. Linear regression was used to fit Ct values against nominal concentrations. Odds ratios for high-risk haplotypes (C-C-T and/or C-C-C at positions 162,215–162,476-163,364) were calculated using the common low-risk haplotypes as reference (sum of A-T-C and C-T-C). For EBV-positive NPC cases, the reference group includes all non-NPC controls for each individual study (present cohort, Xu et al., Hui et al., Lam et al.) [9–11]. Fisher exact tests were used to calculate p-values for SNV and haplotype associations with NPC. For targeted NGS, the p-value threshold for statistical significance was adjusted for the number of evaluated positions using the Bonferroni correction (α = 3.68 × 10− 5). Analyses were conducted using the R statistical software package.

Copyright and License information: The Author(s) ©2022
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A