Gene weights or without gene weights

[QianChwnLyn]

Hi, I would like to ask what the impact is on the results of whether the gene set gs file contains the weight value. I discovered while watching magma tutorials that I did not understand how to calculate. By extracting the p-value of the SNPs for each gene set in the gwas results? Or what impact will it have on my results if I don't calculate the weight value?

[martinjzhang]

Hi @QianChwnLyn

You can use the z scores that the MAGMA software generates.

If you go without the gene weights, the method will lose some power (e.g., 10-30% depending on the dataset).

[schnappi-wkl]

Hi martin， i also encountered the similar issue, i have some genesets associated with milk producting trait of buffalo without corresponding the GWAS database unfortunately. i want to associate these traits with tissue or celltype, could you give me some advices? thanks Schnappi

[martinjzhang]

Hi @schnappi-wkl

It's fine to go without the gene weights. The method will lose some power (e.g., 10-30% depending on the dataset). But the results should be well-calibrated.