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eskederks / eMAGMA-tutorial

A step by step guide on how to use eMAGMA, an approach to conducting eQTL informed gene-based tests.
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issues in eMAGMA GENE-SET ANALYSIS #11

Open changxuling opened 2 months ago

changxuling commented 2 months ago

Hi,

I am trying to run through the tutorial using Amygdala_emagma.genes.raw inside Amygdala_outputs.zip but encountered the attached issue. Could you please kindly help with that? image

Also the eMAGMA Co-expression network files is currently only avaiable for brain tissues. May I know whether it is available for other tissues? if not, could you please kindly share the codes that you have used for the brain tissues?

The last question will be I notice in the paper that the data is from EUR. How does this work for other ethnicity groups?

Thank you.

Cheers Shirley

gerringz commented 1 month ago

Hi Shirley, Happy to share the co-expression files, will organise the transfer. We have generated annotation files for brain tissues and whole blood, however these are only available for EUR ancestry defined in GTEx. I can assist with generation of ancestry-specific annotation files if you have in-house data. Regards, Zac