From f429767fa9b5f221714a8566d7a770529efe0e7f Mon Sep 17 00:00:00 2001 From: Xiangzhen Kong Date: Tue, 28 Jan 2020 14:50:32 +0100 Subject: [PATCH] --adap-permp not for multiple testing correction --adap-permp should be for obtaining permutation-based empirical gene p-values. It's not for multiple testing correction. --- eMAGMA tutorial PART_1.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eMAGMA tutorial PART_1.md b/eMAGMA tutorial PART_1.md index b5df71f..209e6f9 100644 --- a/eMAGMA tutorial PART_1.md +++ b/eMAGMA tutorial PART_1.md @@ -48,7 +48,7 @@ Make sure you return to the eMAGMA folder. To run the association use: --out Amygdala_emagma -The above command indicates: Brain_Amygdala.genes.annot, is the input file for the analysis, P-values are extracted from the MDD GWAS summary data [MDD2018_ex23andMe_emagma.txt]. The effective number of samples is in column Neff. Multiple testing is done using 10,000 adaptive permutations (--adap-permp=10,000). +The above command indicates: Brain_Amygdala.genes.annot, is the input file for the analysis, P-values are extracted from the MDD GWAS summary data [MDD2018_ex23andMe_emagma.txt]. The effective number of samples is in column Neff. Permutation-based empirical gene p-values are estimated using 10,000 adaptive permutations (--adap-permp=10,000). The program also generates a log file [Amygdala_emagma.log]. The log file has summary information of the run, i.e. errors if any, how many genes were read and how many genes have a valid SNP assigned. An inspection of the Amygdala_emagma.log, shows that 1301 genes definitions were read from the annotation file and 1258 genes have valid SNPs in genotype data.