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

Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …

Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20

Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…

Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Guido Hooiveld ★ 4.1k

Hi James, I am likely missing something obvious, but why is the code that I used returning a different number of genes having a GOALL-BP a…

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

I use `minfi` for preprocessing and `DMRcate` for DMR. I like `preprocessFunnorm` (and possibly the XY-interpolated version in the `wateRme…

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

I gave you busted SQL code that returned the central key for the DB rather than the gene IDs. Here's the corrected version. ``` > mgis <- …

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Answer: object 'hdac_targets' not found

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