Hello everyone! I could not find the statistical test which is utilized by TASSEL when running mixed liner model to find SNP-phenotype association. Googling on this topic had no success: The article on TASSEL (https://tassel.bitbucket.io/docs/bradbury2007bioinformatics.pdf) say that F-test is utilized for general linear model, but there is nothing said on mixed liner model. In Google groups (https://groups.google.com/forum/#!topic/tassel/G3gL3eocMHQ) and Biostars (Association Mapping And Fdr (False Discovery Rate) Test?) it is mentioned that TASSEL utilizes nominal test. If I am not mistaken nominal test is chi-square and If so it is confusing what data is in chi-square table? The number of observed SNPs and number expected SNPs affecting trait?
