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GSEA
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
6 weeks ago • updated 5 weeks ago
Gordon
• 0
2
votes
1
reply
216
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 6 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
enee
▴ 10
4
votes
3
replies
238
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 7 weeks ago by
Georg
• 0
9
votes
13
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6.6k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 3 months ago by
ATpoint
★ 4.1k • written 2.1 years ago by
nhaus
▴ 30
0
votes
3
replies
1.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot
GSEA
clusterProfiler
updated 6 months ago by
Fatemeh
• 0 • written 9 months ago by
Cen
• 0
0
votes
1
reply
614
views
choosing rank for GSEA
gsea
DESeq2
updated 6 months ago by
ATpoint
★ 4.1k • written 6 months ago by
Grace.Ciabattoni
• 0
0
votes
0
replies
625
views
using fgsea to compare two datasets
GSEA
fgsea
9 months ago
Cen
• 0
1
vote
1
reply
990
views
How to do GSEA over limma + voom DGE ?
GSEA
voom
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
manuelsokolov
• 0
8 results • Page
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Ask yourself the question how a gene that is exactly the same everywhere adds anything to any analysis. Heatmaps usually take DEGs to infer…
Comment: Extremely small p-values using Limma for proteomic data
by
ATpoint
★ 4.1k
I'd argue that most users, especially the general reader of a paper is interested in a visual representation of the data **and** applied cu…
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
I'd also add that plotting adjusted P-values in the y-axis of the volcano plot is not the recommended way to produce a volcano plot. This h…
Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Votes
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
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