Bioconductor Forum
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
votes
replies
6.9k
views
How to use EnrichGo of Cluster Profiler
EnrichGO
clusterProfiler
updated 3 hours ago by
Carol
written 5.3 years ago by
Carolina
votes
replies
11
views
gscreend for CRISPR analysis
gscreend
CRISPR
6 hours ago
daniela.cecalev
votes
replies
372
views
Choosing between voomLmFit() and DREAM() when they identify very different sets of DEGs
limma
variancePartition
15 days ago • updated 1 day ago
Emmanuel
votes
reply
138
views
DESeq2: Comparing sequencing methods with different sequencing depths
DESeq2
updated 2 days ago by
Michael Love
43k
written 8 days ago by
martin.t
votes
replies
43
views
DGE for two groups with n=1 vs n=many analysis.
edgeR
NOISeq
Bioconductor
DESeq2
2 days ago
Valeriya208
votes
replies
61
views
News:
Post-Conference Events at BioC2026: Workshop and Hackathon
Conference
Bioconductor
BioC2026
4 days ago
laurah ondari
votes
replies
172
views
Calculating PC Loadings on FastMNN Corrected PCs
batchelor
8 days ago • updated 3 days ago
Josephine
votes
replies
53
views
Best Ordb for phytoplankton
rvvgo
GO.db
8 days ago
Teleo
votes
replies
2.0k
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 8 days ago by
Carol
written 2.5 years ago by
mphogan
votes
replies
140
views
News:
EuroBioC2026 Pre-conference events - Registration Open!
Conference
Bioconductor
EuroBioc2026
9 days ago
laurah ondari
votes
replies
93
views
BASIC PRINCIPLES of confunding testing in microbiome data
pcaMethods
MicrobiomeData
maaslin3
10 days ago
pascal.segura
votes
14
replies
743
views
Using duplicateCorrelation with limma/voom for spatial transcriptomics data
limma
standR
SpatialExperiment
11 days ago • updated 8 days ago
Krista
votes
replies
247
views
Error importing q-values into EList from a parquet file
limpa
updated 6 days ago by
Gordon Smyth
53k
written 10 days ago by
Matthew Thornton
390
votes
reply
807
views
News:
The Call for Abstracts for BioC2026 is open!
Bioconductor
Conference
updated 10 days ago by
specificwatchful
written 11 weeks ago by
laurah ondari
votes
replies
101
views
Negative probe values in standR/SpatialExperiment
standR
SpatialExperiment
11 days ago
Krista
votes
reply
137
views
News:
List of Deprecated Packages for Bioc3.23
devel
Devel
Release
Deprecated
release
11 days ago
shepherl
4.3k
votes
replies
2.5k
views
News:
EuroBioC2023 abstract submission is open!
presentation
EuroBioC2023
Conference
community
Bioconductor
written 3.2 years ago by
Maria Doyle
110
votes
replies
2.0k
views
ChAMP functional normalization error "subscript out of bounds"
champ
epic microarray
normalization
minfi
updated 13 days ago by
Qiang
written 7.9 years ago by
Laura
votes
replies
480
views
Can I use the limma duplicateCorrelation function for nested case control study
limma
updated 8 days ago by
Ghostwriter
written 14 days ago by
yuan
votes
replies
93
views
DiffBind - how to dividing DBA objects by chromosomes and perform analyses in DiffBind
CUT&Tag
DiffBind
14 days ago
Chloe
votes
replies
109
views
Issue using barplot function in r
clusterProfiler
Bioconductor
enrichGO
barplot
16 days ago
GA
10
votes
replies
203
views
Pathview not mapping all gene names in diagram
pathview
DESeq2
17 days ago • updated 14 days ago
fonsvandehare
vote
reply
216
views
Diffbind using EdgeR
DiffBind
edgeR
updated 19 days ago by
Gordon Smyth
53k
written 22 days ago by
Nico
vote
replies
2.0k
views
Can't produce a generegiontrack from my txdb anymore
gviz
GenomicFeatures
written 4.7 years ago by
A.J.
20
votes
replies
606
views
DESeq2 single factor multiple levels, log of ratio or ratio of log ?
dese
scrna
scRNAseq
DESeq2
written 28 days ago by
Naomie
votes
replies
125
views
Differential miRNAome analysis for miRNA-generating protein mutant
Normalization
DESeq2
miRNA
DifferentialExpression
23 days ago
jpt8069
votes
replies
358
views
scRNA compositional analysis tools
scRNAseq
scCODA
propeller
scikit
updated 12 days ago by
danymukesha
written 24 days ago by
soumyaya21
votes
reply
205
views
Different GSEA results from same GEO dataset: Salmon vs TopHat pipeline
org.Mm.eg.db
tximport
DESeq2
clusterProfiler
updated 24 days ago by
ATpoint
5.0k
written 25 days ago by
해연
votes
replies
views
Spam:
Productos de Motorsport: Tecnología de Carreras para la Calle
Cepo
25 days ago
Akash
votes
reply
293
views
Blocking vs duplicateCorrelation for unbalanced designs in limma
limma
updated 28 days ago by
Gordon Smyth
53k
written 29 days ago by
A.Barden
20
votes
replies
18
views
Spam:
Can Assignment Helper best service improve grades for college students
BSgenome.Hsapiens.UCSC.hg17.masked
29 days ago
marinasky801
vote
replies
364
views
Permutation analysis/bootstrapping - DESeq2
DESeq2
updated 4 weeks ago by
James W. MacDonald
68k
written 4 weeks ago by
epocr
vote
replies
388
views
A question about limpa - multi level experiment
limpa
multi-level
updated 29 days ago by
Gordon Smyth
53k
written 4 weeks ago by
J Kim
10
votes
replies
127
views
Error in BMIQ initialization
BMIQ
wateRmelon
4 weeks ago
David
votes
reply
209
views
F-statistic cutoff for GSEA
clusterProfiler
GSEA
updated 5 weeks ago by
ATpoint
5.0k
written 5 weeks ago by
siobhan.dietz
votes
replies
176
views
News:
Final call! BioC2026 abstract submissions are closing soon
Bioconductor
BioC2026
Conference
5 weeks ago
laurah ondari
vote
replies
280
views
Is psygenet2r still functional?
psygenet2r
Bioconductor
written 5 weeks ago by
Jon
vote
replies
335
views
How to remove/clean unwanted DEG data before downstream analysis?
DifferentialExpression
limma
updated 5 weeks ago by
James W. MacDonald
68k
written 5 weeks ago by
mishi
vote
replies
343
views
RNA-seq, point-by-point contrasts
edgeR
updated 4 weeks ago by
J Kim
10
written 5 weeks ago by
boczniak767
750
votes
replies
427
views
Is it still possible to do batch correction for my data?
RNASeq
edgeR
6 weeks ago • updated 5 weeks ago
LBJ0744
votes
replies
237
views
News:
The BioC2026 Call for Abstracts deadline has been extended
Bioconductor
BioC2026
Conference
6 weeks ago
laurah ondari
votes
reply
285
views
specifying refColumn in calcNormFactors()
edgeR
limma
updated 6 weeks ago by
Gordon Smyth
53k
written 6 weeks ago by
Nova
votes
reply
364
views
Sex prediction in sesame for EPICV2
sesame
EPICv2manifest
updated 6 weeks ago by
Tim Peters
230
written 6 weeks ago by
poojitha.stemcell
10
votes
replies
198
views
APAlyzer gives zero/NaN matrix?
APAlyzer
6 weeks ago
lynn.hua.lee
votes
replies
405
views
Convergence Issues and Model Selection DESeq2
DESeq2
6 weeks ago
dani.guan.3
votes
replies
1.2k
views
Limma-voom sample weights and impact on DEG numbers
limma
updated 1 day ago by
Salvex
written 4 months ago by
A.Barden
20
votes
replies
463
views
Quick two questions on limpa
limpa
updated 5 weeks ago by
Gordon Smyth
53k
written 6 weeks ago by
J Kim
10
votes
replies
288
views
recursively counting package dependencies
BiocPkgTools
6 weeks ago
Helena
vote
replies
353
views
Subsetting DDS object for individual conditions over time
DESeq2
7 weeks ago • updated 6 weeks ago
70
votes
replies
357
views
tximeta cannot open annotation gtf?
tximeta
Bioconductor
updated 7 weeks ago by
Michael Love
43k
written 7 weeks ago by
lynn.hua.lee
46,826
results
Page
1 of 937
Recent ...
Replies
Answer: How to use EnrichGo of Cluster Profiler
by
Carol
thanks for help!
Comment: Bay area Biotech-Pharma Statistics Workshop, with free R user meetup (Nov 6-8)
by
Ilvas
The Bay Area Biotech Pharma Statistics Workshop is a two day conference dedicated to advancing the practice and impact of statistics within…
Comment: Limma-voom sample weights and impact on DEG numbers
by
Salvex
[Office Painters][1] Dubai Fixit is a trusted choice for businesses seeking high-quality, efficient, and professional painting solutions in…
Comment: Choosing between voomLmFit() and DREAM() when they identify very different sets
by
Emmanuel
Thanks so much for your reply! I'm glad the flat region is not an issue.
I will think carefully about the impact of other potential batch …
Comment: Choosing between voomLmFit() and DREAM() when they identify very different sets
by
Gordon Smyth
53k
The "flat region" is not a concern. You do not need more filtering. voomLmFit() is very robust to filtering.
The increasing spread strongl…
Votes
A: WGCNA automatic vs manual network creation
C: Steep dendrograms and few modules. WGCNA on RNA seq data
Comment: Choosing between voomLmFit() and DREAM() when they identify very different sets
Answer: Choosing between voomLmFit() and DREAM() when they identify very different sets
Answer: Using duplicateCorrelation with limma/voom for spatial transcriptomics data
Awards
• All
Popular Question
to
shepherl
4.3k
Popular Question
to
Gordon Smyth
53k
Popular Question
to
amye107
Popular Question
to
Hervé Pagès
16k
Popular Question
to
Michael Love
43k
Locations
• All
The city by the bay,
8 minutes ago
United States,
14 minutes ago
Chile,
44 minutes ago
United States,
2 hours ago
The Netherlands,
2 hours ago
Traffic: 1159 users visited in the last hour
Content
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy
Policy
version 2.3.6