Conflicts between MetaSKAT and SKATO

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Yuyang Luo

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Feb 7, 2024, 2:21:13 PMFeb 7

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Hi,

I am currently using SKATO for two batches, and using MetaSKAT to meta-analyze them. However, when we merged those results together, it looked strange. I am attaching some results here. For instance,

The p-value of gene TF from MetaSKAT is 7.28E-06, while the p-values from the two batches are 0.00017 and 0.882, respectively, which does not make sense. It would be great if anyone can help me figure out this issue. Thank you.

Best,

Leo

MetaSKAT_SKATO.xlsx

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