I have 187 lines. They were genotyped using 156 snps. I used tassel for running the association analysis. And I need to use FDR to determine the significant markers. Some studies suggest 0.2. I need to know based on what this value is determined.
MLM (EMMAX) can have many false discoveries, MLMM is more specific (Multi Locus Mixed Model), in SVS golden helix can calculate BIC, Regression beta, FDR, Prop. var. explained, and can chose step by step the best results:
multiple PPA
Mod. BIC
Ext. BIC
Bonferroni
Multiple Bonferroni
References:
Segura V, Vihjálmsson BJ, Platt A, Korte A, Seren Ü, et al. (2012) ‘An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations’, Nature Genetics, 44, 825–830.