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27
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DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
shrinkage
DESeq2
contrast
1 day ago
ja569116
• 0
0
votes
1
reply
65
views
limpa analysis advice
limpa
updated 20 hours ago by
Gordon Smyth
53k • written 1 day ago by
SamGG
▴ 360
0
votes
0
replies
21
views
News:
The BioC2026 Sticker Design Contest is Open!
Bioconductor
Conference
1 day ago
laurah ondari
• 0
4
votes
2
replies
139
views
When to use edgeR or limma
edgeR
limma
updated 1 day ago by
Gordon Smyth
53k • written 3 days ago by
abzhang97
• 0
1
vote
3
replies
151
views
Incosistencies in buildSNNGraph() function
scran
seurat
written 7 days ago by
Lucas
• 0
0
votes
2
replies
627
views
A problem occurs when running the monocle2
monocle
written 4 months ago by
yuheng_yang
• 0
0
votes
3
replies
184
views
limpa-blank normalization and Spectronaut's PTM stoichiometry
limpa
updated 2 days ago by
Gordon Smyth
53k • written 3 days ago by
emily.wolfrum
• 0
0
votes
0
replies
33
views
Are individual-mouse-based statistics possible in CellChat?
Bioconductor
CellChat
3 days ago
Omer
• 0
0
votes
1
reply
57
views
Questions about bacon QC and correction on EWAS results
bacon
3 days ago
sup0903
• 0
3
votes
4
replies
190
views
Question about the filterByExpr function inputs in edgeR
RNASeq
filter
design
edgeR
model.matrix
4 days ago • updated 3 days ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
71
views
Development of MSstat workflow to analyze DIA time series data
MSstats
updated 4 days ago by
Gordon Smyth
53k • written 4 days ago by
sithurandi
• 0
0
votes
0
replies
70
views
MSstatsPTM-SpectronauttoMSstatsPTMFormat-failing with TAIR10 Locus Tags: Issue with UniProt-centric protein ID parsing
Bioconductor
MSstatsPTM
4 days ago
srkingwu
• 0
8
votes
8
replies
2.8k
views
Confounded design, batch effect correction (edgeR)
rnaseq
edger
differential gene expression
batch effect
written 7.4 years ago by
Laura
▴ 20
0
votes
0
replies
46
views
Junction CPM via Snapcount and Recount3
snapcount
recount3
5 days ago
henry.tietz
• 0
3
votes
4
replies
315
views
Clarification on counting in Rsubread (featureCounts)
featureCounts
Rsubread
updated 4 days ago by
Gordon Smyth
53k • written 4 weeks ago by
Luca
• 0
0
votes
0
replies
37
views
News:
Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano
GSEABase
pheatmap
Workshop
DESeq2
5 days ago
Frances Turner
▴ 20
0
votes
0
replies
42
views
How to convert .raw data for use in xcms
xcms
5 days ago
Monica
• 0
0
votes
0
replies
67
views
Job:
Open Positions for Doctoral Researchers in Molecular Medicine
JobPosting
5 days ago
rubina.tabassum
• 0
1
vote
0
replies
81
views
News:
Bioconductor Maintainer Application
maintainer
policy
Bioconductor
Devel
devel
8 days ago
shepherl
4.3k
0
votes
1
reply
452
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
written 10 months ago by
info
▴ 10
0
votes
1
reply
326
views
News:
Announcing a New Journal - Bioinformatics Methods and Applications - Now Open for Submissions
Bioconductor
written 6 months ago by
Wei Shi
★ 3.6k
0
votes
2
replies
2.5k
views
ChAMP pipeline error (champ.import)
software error
written 6.8 years ago by
mhebba
• 0
0
votes
1
reply
165
views
Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
updated 10 days ago by
Gordon Smyth
53k • written 10 days ago by
Andrew Pattison
• 0
0
votes
0
replies
112
views
Job:
Jobs at Ensembl
ensembldb
11 days ago
Aleena_Ensembl
▴ 30
0
votes
0
replies
11
views
Spam:
Is there a way to map Excel fields to VCF contacts for accurate conversion?
ComputationalChemistry
Technology
Software
Website
updated 11 days ago by
shepherl
4.3k • written 11 days ago by
witebir963
0
0
votes
0
replies
68
views
Job:
Job:Computational Biologist position at the University of Alabama at Birmingham
hiring
RNASeq
JobPosting
SingleCell
SpatialData
12 days ago
lianov
• 0
2
votes
3
replies
193
views
please provide a BibTeX citation for "Advanced Single-Cell Analysis with Bioconductor"
Bioconductor
written 12 days ago by
Victor
▴ 10
2
votes
4
replies
213
views
Converting Probe IDs to HGNC symbols
Annotation
biomaRt
GEOquery
written 14 days ago by
Manav
▴ 10
0
votes
3
replies
259
views
How to do differential expresion across time serise with edgeR?
edgeR
timecoursedata
updated 14 days ago by
Gordon Smyth
53k • written 15 days ago by
petergrahamclark
▴ 10
2
votes
3
replies
408
views
Guitar R package requires update due to dependency GenomicFeatures
GenomicFeatures
Guitar
txdbmaker
GenomicRanges
written 19 days ago by
ferran.llobet.cabau
▴ 10
0
votes
2
replies
166
views
ATACseq rudimentary questions
ATACSeq
DiffBind
21 days ago • updated 15 days ago
4747
• 0
1
vote
1
reply
203
views
How to install packages such as TCGAbiolinks, SumarizedExperiment?
TCGAbiolinks
SummarizedExperiment
updated 17 days ago by
Gordon Smyth
53k • written 17 days ago by
NewRUser
• 0
0
votes
4
replies
5.5k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.8 years ago by
mauricio.microbiol
• 0
4
votes
2
replies
362
views
Limma-voom sample weights and impact on DEG numbers
limma
25 days ago • updated 12 days ago
A.Barden
▴ 20
0
votes
1
reply
246
views
wgcna module preseravtion taking too long?
WGCNA
updated 25 days ago by
ATpoint
★ 5.0k • written 4 weeks ago by
lamia11me
• 0
0
votes
1
reply
332
views
Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCPlus)
HiC
HiCDCPlus
written 5 weeks ago by
Chaoability
• 0
0
votes
3
replies
287
views
DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
sva
lfcshrink
DESeq2
29 days ago • updated 1 day ago
ja569116
• 0
0
votes
5
replies
2.9k
views
Ensembl site unresponsive via biomaRt
biomaRt
written 9 months ago by
hebda
• 0
0
votes
3
replies
279
views
segfault in edgeR glmQLFit
edgeR
updated 25 days ago by
Gordon Smyth
53k • written 29 days ago by
Mark
• 0
0
votes
4
replies
583
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 12 days ago by
jtsy6383
• 0 • written 4 weeks ago by
Durian
• 0
0
votes
1
reply
247
views
News:
Opportunity to host EuroBioC2026 Preconference workshops!
Conference
Workshop
Bioconductor
written 4 weeks ago by
laurah ondari
• 0
0
votes
1
reply
153
views
NUPOP usage
TOAST
updated 5 weeks ago by
shepherl
4.3k • written 5 weeks ago by
Mohammad
• 0
1
vote
2
replies
349
views
News:
Important: Bioconductor Release 3.22 Delayed
release
written 11 weeks ago by
shepherl
4.3k
0
votes
2
replies
293
views
BiocParallel (and DESeq2) - wrong args for environment subassignment
BiocParallel
DESeq2
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
Benjamin
• 0
0
votes
1
reply
228
views
PTM analysis in LIMPA
limpa
updated 2 days ago by
Gordon Smyth
53k • written 6 weeks ago by
Diego FGR
• 0
1
vote
1
reply
266
views
News:
Upcoming Ensembl API and data access changes - new blog post available
ensembl
mart
biomaRt
ensembldb
written 6 weeks ago by
Ensembl_Jorge
▴ 10
0
votes
2
replies
270
views
problem reading bam files into nucleR
nucleR
updated 6 weeks ago by
James W. MacDonald
68k • written 7 weeks ago by
efoss
▴ 10
0
votes
0
replies
14
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
6 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
TOAST
6 weeks ago
Maya
0
0
votes
0
replies
9
views
Spam:
Career Growth After CCNP Certification Training: Roles, Salaries & Opportunities
ScreenR
6 weeks ago
Maya
0
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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