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 :
category
•
reset
1
vote
1
reply
1.4k
views
Goseq output with too many GO terms per category
go
goseq
goterm
category
updated 6.2 years ago by
Gordon Smyth
51k • written 6.2 years ago by
Juan
• 0
0
votes
3
replies
2.4k
views
Getting Differentially Expressed Genes from GOSeq Categories
goseq
gene ontology
biomart
annotate
category
updated 7.3 years ago by
b.nota
▴ 370 • written 7.4 years ago by
krc3004
▴ 10
0
votes
4
replies
5.2k
views
goseq analysis - extracting list of my genes which are DE in the enriched GO category
GO
Category
goseq
GO
Category
goseq
updated 8.6 years ago by
darshinimamindla
▴ 10 • written 13.2 years ago by
Helen Wright
▴ 10
1
vote
0
replies
1.5k
views
enrichment analysis for gene pairs
go
gostats
category
gsea
9.0 years ago
Hector Corrada Bravo
▴ 60
0
votes
0
replies
1.5k
views
hyperGTest for MSigDB categories
category
gostats
msigdb
hypergeometric test
9.3 years ago
petyuk
▴ 70
0
votes
8
replies
2.3k
views
PFAM Enrichment in GOstats
PFAM
Category
GOstats
updated 9.5 years ago by
Guangchuang Yu
★ 1.2k • written 9.5 years ago by
Iain Gallagher
▴ 930
2
votes
2
replies
1.2k
views
rownames for categoryReshape
Category
updated 10.0 years ago by
Martin Morgan
25k • written 10.0 years ago by
alison.sara.waller
• 0
1
vote
0
replies
1.3k
views
how to fetch GO categories from Chinese hamster genome
GO
Category
goseq
10.2 years ago
upendra kumar devisetty
▴ 30
0
votes
1
reply
1.6k
views
GO enrichment
GO
Category
goseq
GO
Category
goseq
10.3 years ago • updated 10.2 years ago
Guest User
★ 13k
0
votes
1
reply
1.8k
views
snpStats reference allele used in genetic associations?
SNP
Category
snpStats
SNP
Category
snpStats
updated 10.5 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.5 years ago by
Guest User
★ 13k
0
votes
0
replies
1.9k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
10.6 years ago
Magda Price
▴ 60
0
votes
8
replies
5.1k
views
ComBat: 3 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
updated 10.6 years ago by
Steve Lianoglou
★ 13k • written 10.6 years ago by
Guest User
★ 13k
0
votes
0
replies
2.1k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
10.7 years ago
W. Evan Johnson
▴ 860
0
votes
0
replies
1.8k
views
ComBat: 2 adjustment variables & continuous adjustment variables
GO
Category
sva
GO
Category
sva
10.7 years ago
Magda Price
▴ 60
0
votes
0
replies
1.9k
views
R pathview and mouse
Category
pathview
Category
pathview
10.8 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
2.1k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription
Annotation
Normalization
GO
hgu133plus2
affy
PROcess
Category
Transcription
updated 10.9 years ago by
Federico Lasa
▴ 80 • written 10.9 years ago by
María Maqueda González
▴ 20
0
votes
4
replies
4.0k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Annotation
Normalization
hgu133plus2
affy
PROcess
Category
Annotation
Normalization
affy
updated 10.9 years ago by
James W. MacDonald
67k • written 10.9 years ago by
Guest User
★ 13k
0
votes
1
reply
1.2k
views
GSEABase error parsing msigdb_v4.0.xml
Category
Category
updated 11.0 years ago by
Martin Morgan
25k • written 11.0 years ago by
Milica Ng
▴ 10
0
votes
0
replies
1.5k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray
limma
Category
CAMERA
GSVA
Microarray
limma
Category
CAMERA
GSVA
11.0 years ago
Gordon Smyth
51k
0
votes
0
replies
1.3k
views
enrichment packages that accept t-stat (or related stat) as input
Microarray
Proteomics
limma
Category
CAMERA
GSVA
Microarray
Proteomics
limma
Category
11.0 years ago
Pekka Kohonen
▴ 190
0
votes
1
reply
1.1k
views
Which package I should use
Sequencing
Category
Sequencing
Category
updated 11.2 years ago by
Pet Chiang
▴ 30 • written 11.2 years ago by
Xiaoben Jiang
▴ 10
0
votes
7
replies
5.0k
views
Simple pathway enrichment analysis for gene lists
Microarray
Category
gage
KEGGREST
ROntoTools
Microarray
Category
gage
KEGGREST
ROntoTools
updated 11.2 years ago by
Paul Shannon
▴ 470 • written 11.2 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.5k
views
topGO analysis returns different gene counts for category than given for non-model organism
GO
Category
topGO
GO
Category
topGO
updated 11.2 years ago by
Valerie Obenchain
★ 6.8k • written 11.2 years ago by
Diana Toups Dugas
▴ 20
0
votes
0
replies
1.4k
views
new window cairo bundle Re: [Rd] R/Sweave/cairo/freetype bug fix.
Category
BEAT
Category
BEAT
11.4 years ago
Hin-Tak Leung
▴ 30
0
votes
0
replies
1.1k
views
Diff Bind consultation
Category
DiffBind
Category
DiffBind
11.5 years ago
Rory Stark
★ 5.2k
0
votes
0
replies
1.1k
views
RE : ChIPpeakAnno_2.8.0 assignCromosomeRegion
annotate
Category
ChIPpeakAnno
annotate
Category
ChIPpeakAnno
11.5 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.3k
views
[Rd] R/Sweave/cairo/freetype bug fix.
Category
Category
updated 11.6 years ago by
Simon Urbanek
▴ 60 • written 11.6 years ago by
Hin-Tak Leung
▴ 30
0
votes
6
replies
1.3k
views
Extract microarray data for genes identified by GO analysis
Microarray
GO
Category
Microarray
GO
Category
updated 11.7 years ago by
James W. MacDonald
67k • written 11.7 years ago by
Guest User
★ 13k
0
votes
2
replies
1.7k
views
GSEABase error parsing msigdb_v3.1.xml
GO
Infrastructure
hgu95av2
Biobase
annotate
graph
Category
AnnotationDbi
BiocGenerics
GO
updated 11.8 years ago by
Martin Morgan
25k • written 11.8 years ago by
Lina Hultin-Rosenberg
▴ 80
0
votes
2
replies
1.4k
views
Difficulties in using the mgsa package for Gene Set Analysis
GO
rat2302
Category
mgsa
GO
rat2302
Category
mgsa
updated 11.8 years ago by
Sebastian Bauer
▴ 60 • written 11.8 years ago by
Guest User
★ 13k
0
votes
0
replies
911
views
ChIPpeakAnno
Annotation
Category
ChIPpeakAnno
Annotation
Category
ChIPpeakAnno
12.0 years ago
Julie Zhu
★ 4.3k
0
votes
1
reply
1.0k
views
HyperGTest 'count' value
Annotation
Category
Annotation
Category
12.0 years ago
Mary Kindall
▴ 70
0
votes
0
replies
778
views
strange results with edgeR::goodTuring
Category
edgeR
Category
edgeR
12.2 years ago
Gordon Smyth
51k
0
votes
2
replies
1.1k
views
strange results with edgeR::goodTuring
Category
edgeR
Category
edgeR
updated 12.2 years ago by
Gordon Smyth
51k • written 12.2 years ago by
Francois Pepin
▴ 80
0
votes
3
replies
2.1k
views
oligo and pd.aragene.1.1.st annotation
Annotation
limma
Category
pdInfoBuilder
Annotation
limma
Category
pdInfoBuilder
updated 12.3 years ago by
Marc Carlson
★ 7.2k • written 12.3 years ago by
Stephen Rolfe
▴ 20
0
votes
2
replies
1.1k
views
easyRNAseq question
Category
DESeq
easyRNASeq
Category
DESeq
easyRNASeq
updated 12.3 years ago by
Wolfgang Huber
★ 13k • written 12.4 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
0
votes
3
replies
1.5k
views
GOstats - internal filtering?
Annotation
GO
hgu133plus2
GOstats
Category
Annotation
GO
hgu133plus2
GOstats
Category
updated 12.6 years ago by
James W. MacDonald
67k • written 12.6 years ago by
Andrew Jaffe
▴ 120
0
votes
0
replies
1.3k
views
Biological Pathway Database
Transcription
Pathways
Category
Transcription
Pathways
Category
12.6 years ago
Gita Singh
▴ 10
0
votes
3
replies
2.0k
views
Affymetrix Intronic Normalization Control Probes Differentially Expressed?
probe
limma
Category
probe
limma
Category
updated 12.6 years ago by
James W. MacDonald
67k • written 12.6 years ago by
Alexandra Muñoz
▴ 10
0
votes
0
replies
1.3k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation
GO
Cancer
Apis mellifera
BSgenome
Biostrings
Category
BSgenome
rtracklayer
GO
12.7 years ago
Matthew Young
▴ 50
1
vote
0
replies
2.3k
views
TopGO p-values VS DAVID p-values
Microarray
GO
Category
topGO
Microarray
GO
Category
topGO
12.8 years ago
Paul Geeleher
★ 1.3k
0
votes
1
reply
1.8k
views
PFAM gene enrichment test using GOstats and Category
SNP
Annotation
GO
Organism
affy
GOstats
Category
SNP
Annotation
GO
Organism
affy
updated 12.8 years ago by
Davis, Wade
▴ 350 • written 12.9 years ago by
Henrik Hjarvard de Fine Licht
▴ 10
0
votes
1
reply
2.4k
views
PFAM gene enrichment test using GOstats and Category
Annotation
GO
Organism
GOstats
Category
Annotation
GO
Organism
GOstats
Category
updated 13.0 years ago by
Marc Carlson
★ 7.2k • written 13.0 years ago by
Henrik De Fine Licht
▴ 10
0
votes
2
replies
1.9k
views
retrieve the level for a GO category
GO
Category
GO
Category
updated 13.0 years ago by
Martin Morgan
25k • written 13.0 years ago by
Biase, Fernando
▴ 150
0
votes
9
replies
1.9k
views
problem with GO terms
GO
GOstats
Category
GO
GOstats
Category
updated 13.0 years ago by
James W. MacDonald
67k • written 13.0 years ago by
Ina Hoeschele
▴ 620
0
votes
0
replies
1.2k
views
goSeq error (steve Shen)
GO
Category
edgeR
goseq
GO
Category
edgeR
goseq
13.0 years ago
Alicia Oshlack
▴ 100
0
votes
4
replies
2.1k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
limma
Category
edgeR
limma
Category
edgeR
updated 13.1 years ago by
Emanuel Heitlinger
▴ 30 • written 13.1 years ago by
Gordon Smyth
51k
0
votes
0
replies
1.2k
views
edgeR - coefficients in 3-factor experiment, complex contrasts and decideTestsDGE
Category
edgeR
Category
edgeR
13.1 years ago
Emanuel Heitlinger
▴ 30
0
votes
2
replies
2.3k
views
RNA seq analysis of Arabidopsis genome
GO
Category
goseq
GO
Category
goseq
updated 13.1 years ago by
Matthew Young
▴ 50 • written 13.2 years ago by
Divya, D.
▴ 10
0
votes
0
replies
1.6k
views
I: R: R: R: Probe-level analysis of exon arrays using xps
Annotation
Normalization
Preprocessing
Breast
Prostate
probe
GLAD
Category
xps
Annotation
13.2 years ago
Lavorgna Giovanni
▴ 80
50 results • Page
1 of 1
Recent ...
Replies
Comment: Problem at champ.load
by
icecreamlover
• 0
Hello! Were you able to figure this out? I am running into the same error!
Comment: ChAMP - obtaining beta values using EPICv2 annotation
by
icecreamlover
• 0
Hello, Were you able to fix the error? I used the same document and I am running into the same error. I am curious if you have any feedba…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Adam
• 0
Can this please be revisited and corrected ASAP? I'm encountering the same issue, using a slightly more modern version of R (4.1.0). It s…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Votes
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Awards
• All
Popular Question
to
Guido Hooiveld
★ 4.1k
Popular Question
to
Gordon Smyth
51k
Popular Question
to
shepherl
4.1k
Supporter
to
Paul Harrison
▴ 100
Popular Question
to
Mikhail Dozmorov
▴ 30
Locations
• All
France,
12 minutes ago
United States,
14 minutes ago
Denmark,
20 minutes ago
San Diego,
21 minutes ago
United States,
48 minutes ago
Traffic: 664 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