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GSEA_internal
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leading edge analysis clusterProfiler DOSE custom GSEA
clusterprofiler
DOSE
GSEA_internal
USER_DATA
leading edge Analysis
8.1 years ago
Riba Michela
▴ 90
1 result • Page
1 of 1
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Comment: Adjusted p-values become NA when sub-setting samples
by
txema.heredia
• 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells
by
Michael Love
42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Fahd
• 0
Thanks for looking into this. This issue results in the incorrect usage of multiple ORA software including EnrichR.
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
Yes, I understand the implications of replacing the `OrgDb` packages in release. Maybe an upload to the annotationHub or GitHub could be an…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
Thanks for following up with NCBI. I can change the code to query the correct column. It's up to somebody with a higher pay scale than mine…
Votes
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
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