Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
GSEa
•
reset
0
votes
13
replies
2.2k
views
Gage and setp argument
gsea
gage
8.0 years ago
peter.chernek
• 0
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 7.5 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
rubi
▴ 110
9
votes
6
replies
5.5k
views
GSEA-like enrichment score calculation
GSEA
enrichment analysis
gseabase
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Matthias Z.
▴ 20
0
votes
5
replies
1.7k
views
gene set (enrichment) analysis
gsea
gsa
updated 8.1 years ago by
Axel Klenk
★ 1.0k • written 8.2 years ago by
Bogdan
▴ 670
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea
gsva
ssgsea
6.3 years ago
jaison75
▴ 20
3
votes
3
replies
1.6k
views
Enrichment Analysis with only GeneSymbols
R
GSEA
rna-seq
scRna-Seq
updated 5.2 years ago by
Peter Langfelder
★ 3.0k • written 5.2 years ago by
hamza_karakurt
▴ 50
0
votes
3
replies
1.8k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
csijst
• 0
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
Robert Castelo
★ 3.3k • written 8.5 years ago by
jacorvar
▴ 40
2
votes
4
replies
3.0k
views
Arguments for camera (gene set analysis)
camera
GSEA
updated 8.2 years ago by
Steve Lianoglou
★ 13k • written 8.2 years ago by
claire.n.levy
▴ 10
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 9.4 years ago by
Levi Waldron
★ 1.1k • written 9.4 years ago by
kaushal Raj Chaudhary
▴ 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
Gordon Smyth
50k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
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
Gordon Smyth
50k • written 5.0 years ago by
Biologist
▴ 110
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 12 months ago by
ATpoint
★ 4.1k • written 7.8 years ago by
EJ
▴ 20
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
predeus
• 0 • written 9.2 years ago by
Nemo
▴ 80
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
ATpoint
★ 4.1k • written 2.2 years ago by
nhaus
▴ 30
0
votes
1
reply
2.5k
views
ClusterProfiler can't load gmt file
GSEA
clusterprofiler
gmt
updated 7.7 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
sarah.blackstone7734
• 0
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea
gsea
updated 7.3 years ago by
alserg
▴ 260 • written 7.3 years ago by
rubi
▴ 110
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
Luo Weijun
★ 1.6k • written 9.1 years ago by
Tom
• 0
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
Aaron Lun
★ 28k • written 8.9 years ago by
svlachavas
▴ 830
1
vote
2
replies
908
views
giving weight to DEG from limma output
limma
GSEA
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Shamim Sarhadi
▴ 20
0
votes
4
replies
1.9k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 7.6 years ago by
Monther Alhamdoosh
▴ 40 • written 7.6 years ago by
yingchen
• 0
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 1 day ago by
Chris
• 0 • written 7.4 years ago by
Pekka Kohonen
▴ 190
0
votes
7
replies
2.1k
views
Statistic for GSA
gsea
concept
gsa
updated 7.3 years ago by
Pekka Kohonen
▴ 190 • written 7.3 years ago by
Lluís Revilla Sancho
▴ 730
0
votes
3
replies
2.3k
views
topGO - treating up- and down-regulated genes separately
topGO
GSEA
pathway analysis
updated 7.2 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.2 years ago by
predeus
• 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
Guido Hooiveld
★ 3.9k • written 7.1 years ago by
danielle.newby
• 0
0
votes
1
reply
1.9k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 7.0 years ago by
Luo Weijun
★ 1.6k • written 7.0 years ago by
snishtala03
• 0
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
bmreilly
• 0
0
votes
1
reply
818
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA
Qusage
5.2 years ago
Diana
▴ 10
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
Dharmesh D Bhuva
• 0 • written 5.2 years ago by
Pietro
▴ 40
2
votes
2
replies
3.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler
GSEA
geneList
updated 4.8 years ago by
Ludwig Geistlinger
▴ 70 • written 4.9 years ago by
lucap
• 0
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.0 years ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
rocanja
▴ 60
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea
ssgsea
gsva
pathways
updated 3.8 years ago by
Robert Castelo
★ 3.3k • written 3.8 years ago by
igor
▴ 40
0
votes
1
reply
817
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO
GSEA
3.4 years ago
lessismore
▴ 20
2
votes
1
reply
981
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 0
0
votes
1
reply
621
views
choosing rank for GSEA
gsea
DESeq2
updated 6 months ago by
ATpoint
★ 4.1k • written 6 months ago by
Grace.Ciabattoni
• 0
7
votes
6
replies
2.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 16 months ago by
Gordon Smyth
50k • written 17 months ago by
nhaus
▴ 30
0
votes
3
replies
1.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA
GSVA
updated 18 months ago by
rocanja
▴ 60 • written 22 months ago by
João
• 0
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC
DESeq2
GSEA
voom
limma
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
Yang Shi
▴ 10
0
votes
2
replies
362
views
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
3
replies
919
views
system.file() failed to load .gmt file.
pathwayPCA
Gsea
updated 18 months ago by
gabriel.odom
• 0 • written 18 months ago by
Mikołaj Mierzejewski
• 0
0
votes
1
reply
1.1k
views
GSEA using custom GO annotations
RNASeq
GSEA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
jms2520
▴ 10
0
votes
2
replies
3.3k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
22 months ago
Bhavana
• 0
4
votes
3
replies
239
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 7 weeks ago by
Georg
• 0
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
2
votes
3
replies
946
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 16 months ago by
belinda.phipson
▴ 40 • written 16 months ago by
Lukas
• 0
1
vote
1
reply
993
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
1
vote
5
replies
2.1k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 6.8 years ago by
alserg
▴ 260 • written 6.8 years ago by
shawn.w.foley
• 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
Andrew_McDavid
▴ 270 • written 6.8 years ago by
siajunren
• 0
1
vote
1
reply
1.1k
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray
GSEA
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
Sanches
• 0
0
votes
2
replies
1.6k
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA
GO
goSlim
6.7 years ago • updated 6.6 years ago
maeva.mollion
• 0
50 results • Page
1 of 1
Recent ...
Replies
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?
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
Thank you James! This worked to fix the p-values. However, the plot still looks one-sided... any idea what's going on with the left side?…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
That ll be helpful. Thank you.
Votes
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
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards
• All
Popular Question
to
neilzhao
▴ 30
Popular Question
to
ATpoint
★ 4.1k
Teacher
to
Michael Love
42k
Popular Question
to
Haibo Liu
• 0
Popular Question
to
HS
▴ 10
Locations
• All
WEHI, Melbourne, Australia,
5 minutes ago
Australia,
30 minutes ago
United States,
31 minutes ago
United States,
57 minutes ago
United States,
1 hour ago
Traffic: 460 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6