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go enrichment
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2.2k
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GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment
gene ontology
goseq
go
4.6 years ago
Raito92
▴ 60
0
votes
0
replies
998
views
GOSemSim - slow for BP terms
gosemsim
go enrichment
go semantic similarity
5.4 years ago
nooshin
▴ 300
2
votes
6
replies
1.9k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 years ago by
jgg
• 0
0
votes
1
reply
2.4k
views
Different results come from GO enrichment analysis with ENSEMBL ID and ENTREZID as keyTypes
clusterprofiler
go enrichment
functional enrichment
updated 5.5 years ago by
Guangchuang Yu
★ 1.2k • written 5.5 years ago by
Jack
• 0
0
votes
1
reply
1.2k
views
TopGO ks test using a score different from p-value
topgo
ks
score
kolmogorov-smirnov test
go enrichment
updated 5.8 years ago by
Lluís Revilla Sancho
▴ 730 • written 5.8 years ago by
eagomezc
• 0
0
votes
0
replies
939
views
GOseq No Underrepresented Categories
goseq
go enrichment
5.9 years ago
mart1139
• 0
1
vote
1
reply
1.5k
views
enrichGO (clusterProfiler) produces different results
chipseq
go enrichment
clusterprofiler
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
Javier Pérez Florido
▴ 840
0
votes
2
replies
3.7k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2
goseq
rnaseq
go enrichment
differential gene expression
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
josef.oeckl
• 0
4
votes
4
replies
3.8k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 6 weeks ago by
jandrade
• 0 • written 6.4 years ago by
Huang, Lei [BSD] - CRI
▴ 20
3
votes
8
replies
2.1k
views
How does the org.Dm.eg.db package deal with NOT annotation qualifiers when annotating genes to GO?
org.dm.eg.db
gene ontology
go enrichment
annotation
NOT
updated 7.1 years ago by
Valerie Obenchain
★ 6.8k • written 7.2 years ago by
triZZla
• 0
0
votes
1
reply
1.1k
views
TopGO Drosophila ananassae
go enrichment
topgo
d.ananassae
updated 7.8 years ago by
James W. MacDonald
65k • written 7.8 years ago by
koeniger
▴ 10
3
votes
1
reply
2.1k
views
Tools for GO term enrichment in prokaryotes
bacteria
GO enrichment
updated 8.8 years ago by
Marc Carlson
★ 7.2k • written 8.8 years ago by
ksw
▴ 20
12 results • Page
1 of 1
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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