the order genes in the gene list on the topGO
hello there
I work with topGO for the analysis of gene enrichment. I discovered that if the order of genes changes in the gene list, the results of p-values also change. I don't know how to order the genes in my gene list to make the results logical.
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Ram
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azadeh.taati •
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azadeh.taati •
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How big are these changes? I've not noticed that before, so I would run a quick permutation test. Randomly order your gene list using the
samplefunction, and run the test 100-1000 times to quantify how often you lose significance around your results.Otherwise, random input order seems like the most fair way to me.
I would also maybe check out if this gene order issue is found in other tools, like g:profiler2 for example.