Showing : gsea • reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.5 years ago by ★ 3.3k • written 8.5 years ago by ▴ 40
9
votes
6
replies
5.5k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 7.9 years ago by 50k • written 7.9 years ago by ▴ 20
9
votes
13
replies
6.6k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.2 years ago by ▴ 30
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 9.4 years ago by ★ 1.1k • written 9.4 years ago by ▴ 10
8
votes
5
replies
3.5k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 110
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 12 months ago by ★ 4.1k • written 7.8 years ago by ▴ 20
7
votes
6
replies
2.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 17 months ago by ▴ 30
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 60
5
votes
7
replies
2.6k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 10
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma mroast GSEA GO illumina human ht-12 v4
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
4
votes
3
replies
238
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 7 weeks ago by • 0
4
votes
1
reply
3.3k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.6 years ago by ▴ 260 • written 6.6 years ago by ▴ 30
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
3
votes
3
replies
1.6k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 50
2
votes
4
replies
3.0k
views
Arguments for camera (gene set analysis)
camera GSEA
updated 8.2 years ago by ★ 13k • written 8.2 years ago by ▴ 10
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
7.3 years ago Pekka Kohonen ▴ 190
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea gsea
updated 7.3 years ago by ▴ 260 • written 7.3 years ago by ▴ 110
2
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.3 years ago by • 0 • written 5.2 years ago by ▴ 40
2
votes
2
replies
3.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.8 years ago by ▴ 70 • written 4.9 years ago by • 0
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 40
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.8 years ago cabezasdelafuented ▴ 10
2
votes
1
reply
981
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by • 0
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 21 months ago by 50k • written 21 months ago by ▴ 10
2
votes
4
replies
1.6k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 20
2
votes
1
reply
216
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 6 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
2
votes
3
replies
918
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 18 months ago by • 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago giuseppe0525 • 0
2
votes
3
replies
944
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
2
votes
2
replies
4.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.1 years ago by ★ 1.2k • written 6.2 years ago by • 0
1
vote
5
replies
2.1k
views
FGSEA only runs with <1000 permutations
fgsea gsea
updated 6.8 years ago by ▴ 260 • written 6.8 years ago by • 0
1
vote
1
reply
1.2k
views
Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
GSEA PAGE microarray differential gene expression pathway analysis
updated 7.1 years ago by ★ 3.9k • written 7.1 years ago by • 0
1
vote
0
replies
1.4k
views
enrichment analysis for gene pairs
go gostats category gsea
8.5 years ago Hector Corrada Bravo ▴ 60
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.3 years ago Stane ▴ 40
1
vote
2
replies
2.1k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 7.2 years ago by • 0 • written 9.2 years ago by ▴ 80
1
vote
1
reply
990
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
0
replies
1.3k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea ncrna coexpression gene set analysis gene set testing
8.0 years ago m.fletcher ▴ 20
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.2 years ago jaison75 ▴ 20
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.5 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
1
vote
2
replies
908
views
giving weight to DEG from limma output
limma GSEA
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.0 years ago by 50k • written 6.0 years ago by ▴ 20
1
vote
1
reply
1.1k
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray GSEA
updated 6.7 years ago by 50k • written 6.7 years ago by • 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
0
votes
1
reply
602
views
GSA type of input data
GSEA GSA vst
updated 16 months ago by 42k • written 16 months ago by ▴ 30
0
votes
1
reply
2.3k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.5 years ago giuseppe0525 • 0
0
votes
6
replies
2.7k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage gsea rnaseq
updated 9.0 years ago by ★ 1.6k • written 9.1 years ago by • 0
0
votes
0
replies
1.1k
views
GSEA with variant proportions as input
GSEA Variant Proportions Input
8.7 years ago manali.rupji • 0
0
votes
5
replies
1.7k
views
gene set (enrichment) analysis
gsea gsa
updated 8.1 years ago by ★ 1.0k • written 8.2 years ago by ▴ 670
0
votes
13
replies
2.2k
views
Gage and setp argument
gsea gage
8.0 years ago peter.chernek • 0
0
votes
1
reply
2.5k
views
ClusterProfiler can't load gmt file
GSEA clusterprofiler gmt
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by • 0
50 results • Page 1 of 1
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Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Votes
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
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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