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Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k

If you want to comment on an answer, please choose ADD COMMENT rather than ADD ANSWER, since you are not in fact adding an answer. ``` uni…

Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0

In fact, I used the BP ontology and I am using gene symbols rather than identifiers (IDs). Is there a way to verify how many genes from the…

Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k

In the other thread I pointed out that filtering on the p-value AND the logFC is fraught because you are mixing population parameter estima…

Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k

The way you are doing it includes all three ontologies. Unless you used "ALL" as the ontology, the number of genes annotated should be less…

Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10

Thank you very much for helping a beginner. To your point, I did that, so there are two pieces of evidence which don't quite compute: If …

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Answer: object 'hdac_targets' not found

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