Links of MX Li's tools:
The Genetic Type I error calculator (GEC) is a Java-based application developed to address multiple-testing issue with dependent Single-nucleotide polymorphisms (SNPs). The core part is a new measure of effective number of independent tests Me , which is more robust than available methods [See the figure below]. Based on this new measure, several popular multiple-testing methods including Bonferroni, Holm, Simes correction was improved to evaluate significance level of SNP p-values in genome-wide association studies. A standalone version of this tool was provided to process large datasets on users’ local computers and an on-line version (GEC, http://statgenpro.psychiatry.hku.hk/GEC) was made for users to quick handle a SMALL dataset conveniently.

When may you need GEC to help you?

Want to know

  • the independent number of tests or redundancy degree in a set of dependent SNPs.
  • the p-value thresholds to declare significant SNPs for association in a set of dependent p-values.

Comments and suggestions are welcome, please e-mail limx54@yahoo.com

Reference:
Li MX, Yeung JM, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012 May;131(5):747-56.
Miao-xin Li, Juilian Yeung Department of Psychiatry, The University of Hong Kong, All rights reserved