Please also read this Nature Biotech primer How does multiple testing correction work? The idea of the FDR is to try to achieve the smallest possible fraction of false signals among all those that appear to be true. Therefore, I was thinking to performed false discovery rate correction with the bootstrap method. FDR: We are testing many hypotheses (in a similar way). Notes. The idea In particular, I have several complete genomes of different species and I am testing whether the genes of one species (foreground) could be under positive selection. Browse other questions tagged hypothesis-testing statistical-significance multiple-comparisons false-discovery-rate or ask your own question. We want to know which ones are likely to be true. False discovery rate (FDR), a new type of multiple tests correction Due to the issues discussed above, multiple tests correction of the classical type are not commonly used in analysis of microarray data these days. Instead, false discovery rate (FDR) has become a standard for multiple tests correction in microarray data analysis. I compared the same null vs alternative model for each gene family, independently. Multiple tests, Bonferroni correction, FDR – p.6/10 pvalues adjusted for multiple hypothesis testing to limit FDR. Featured on Meta Goodbye, Prettify. Deep understanding of p-value, FDR and q-value is not trivial, and many biologists are misusing and/or misinterpreting them. (see Benjamini, Krieger and Yekuteli) •Methods for addressing multiple testing (FWER and FDR) •Deﬁne the multiple testing problem and related concepts. A number of corrections exist for p-values in multiple hypothesis testing (ie: transcriptomics datasets) such as FDR or Bonferroni correction. If there is prior information on the fraction of true hypothesis, then alpha should be set to alpha * m/m_0 where m is the number of tests, given by the p-values, and m_0 is an estimate of the true hypothesis. For biologists’ sake, I will use an example of gene expression. The multiple comparison problem in GWAS: Bonferroni correction, FDR control, and permutation testing 19 Oct 2015 If you are unfamiliar with some terms mentioned in this post, Wikipedia is a good place for quick references.