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ClusterProfiler
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2
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13
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439
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Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
18 days ago • updated 15 days ago
fernanda.backsouza
▴ 10
1
vote
3
replies
872
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 15 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
2
votes
2
replies
195
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
sansan
• 0
1
vote
2
replies
147
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
23 days ago
Ana
• 0
2
votes
2
replies
202
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
27 days ago
julia_mcdonough
• 0
0
votes
1
reply
164
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 25 days ago by
Guido Hooiveld
★ 3.9k • written 29 days ago by
Lucie
• 0
1
vote
1
reply
120
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
fernanda.backsouza
▴ 10
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Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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