Hi all, I have used MAGMA as implemented in FUMA to run a gene-based analysis, using GWAS summary statistics. I now have a certain number of significant genes, in different regions compared to the ones that were significant in the GWAS. I looked at MAGMA paper and it seems it used mean or top statistics from the SNPs one provides, so how come some extra genes are significant now? Shouldn't the statistics have been calculated based on the input list of SNPs? I would really appreciate any help about this.
Thank you very much