fgsea significant result
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Chris ▴ 10
@3fdb6f97
Last seen 3 days ago
United States

Hi all,

fgseaRes <- fgsea(pathways = c2_list, stats = stats, minSize=15, maxSize=500)
significantResults <- fgseaRes[fgseaRes$padj < 0.25, ]

The significantResults changes everytime I run this chunk. Maybe because of permutation. So the significant pathways change, so I can't say which pathways are significant. Would you please have a suggestion? Thank you so much!

fgsea • 253 views
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ATpoint ★ 4.2k
@atpoint-13662
Last seen 2 hours ago
Germany

Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient.

See Why does GSEA on edgeR results for randomized samples give highly significant p-values?

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Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, their result is inconsistent with my result. I plan to further narrow down pathways from significant pathways so I set padj < 0.25. From Gordon answers, seem p value from fgsea is not significant as it is. I tried the function he suggested: camera(). The pathways I got were different with fgsea. I would like to find which pathways are different between 2 conditions so do you think camera() is the best choice? We also have other method for pathway analysis like gene set variation analysis.

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