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Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
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12 days ago • updated 11 days ago
Assa Yeroslaviz
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19 days ago • updated 17 days ago
boczniak767
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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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