MAGMA Gene-Set Analysis top 10 result list

[kongxia...@gmail.com]

In the MAGMA result part, top gene sets are shown. There are some words on multiple testing correction: "The table displays the top the 10 significant gene sets with a maximum of Pbon < 0.05."

I found that top 10 sets are always shown, no matter one can or cannot survive the correction. 

Sometimes the sentence seems a bit misleading. I found in one recent paper, that the authors seems to have considered the top 10 sets as significant sets after correction. It's in the supplemental table of this preprint https://www.biorxiv.org/content/early/2018/10/26/454660

In case where just the top 10 are shown, I think there is no need to metioned the correction threshold. 

If I am wrong, please correct me. Thanks. 

[Kyoko Watanabe]

Hi,

The gene set results are shown for significant SNPs with Pbon<0.05 and if there are <10 significant gene sets, maximum of 10 top significant gene sets are shown.

I'm sorry the description above is wrong, I'll update them.

Best,

Kyoko

[Xiangzhen Kong]

Hi Kyoko, 

Thanks so much for your confirmation. 

Best,

xiangzhen