Hi, everyone, I am using R clusterProfiler package to do GSEA analysis. Following is my code,
GSEA_GO_BP <- GSEA(cor_sort,
exponent = 1,
nPerm = 1000,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 1,
pAdjustMethod = "BH",
seed=FALSE,
TERM2GENE=GO_BP)
I got one question. No matter whether I set seed TRUE or FALSE, GSEA results always changed. I just can't get a reproducible result. Did i set seed in a wrong way? I also see someone else posted the same question, but still no answer.
Thanks in advance.
•
written
by
mthuang.nj •
hey! I had the same issue and I fixed it by adding set.seed(1234) before the function, and then seed = T within the function. You should get the same results now.
set.seed(1234)
GSEA_GO_BP <- GSEA(cor_sort,
exponent = 1,
nPerm = 1000,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 1,
pAdjustMethod = "BH",
seed=TRUE,
TERM2GENE=GO_BP)
•
written
by
brivero •
If this doesn't solve the issue, I strongly recommend to alert the author of the package directly. Actually, I suspect it's a problem with the fgsea algorithm, according to this issue, the solution proposed by brivero should hold up.
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Have you been able solve it? I am having the same issue, and I think it's really important. Every time I run it GSEA using GO and cluster profiler, it give me a different set of enrichment. Please let me know if you figured it out. That will be a great help! Thank you!
Sorry, I still don't know how to figure it out.