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DeplanckeLab / dgrpool_web

DGRPool is a web application designed to serve as a comprehensive repository for Drosophila Genetic Reference Panel (DGRP) phenotyping datasets.
GNU General Public License v3.0
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Review 1 - Improve the GWAS results #29

Open VincentGardeux opened 3 months ago

VincentGardeux commented 3 months ago

We agree with reviewer 1 that normalizing the data could potentially improve the GWAS results. Thus, we plan to explore the implementation of this option and assess its impact on the overall results. We will also investigate replacing the ANOVA test with a KRUSKAL test. Instead of upfront data normalization, we will consider using the PLINK –pheno-quantile-normalize option. Both options will be compared on a set of phenotypes where we can analyze the output (i.e., for phenotypes where we expect to find specific variants), to determine whether these strategies enhance the detection power.

VincentGardeux commented 2 weeks ago

This is done. I've recomputed the results with different normalization and one work slightly better than the others.

We need to organize to update all results. As well as in the DB