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 :
Limma
•
reset
1
vote
4
replies
239
views
Bulk RNAseq analysis for
DESeq2
RNASeq
edgeR
limma
3 days ago • updated 2 days ago
Mariami
• 0
4
votes
2
replies
400
views
When to use edgeR or limma
edgeR
limma
updated 27 days ago by
Gordon Smyth
53k • written 29 days ago by
abzhang97
• 0
0
votes
2
replies
383
views
Combining two proteomics datasets with limpa
limpa
ProteomicsWorkflow
limma
5 weeks ago • updated 22 days ago
Andrew Pattison
• 0
5
votes
3
replies
639
views
Limma-voom sample weights and impact on DEG numbers
limma
written 7 weeks ago by
A.Barden
▴ 20
0
votes
4
replies
659
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 5 weeks ago by
jtsy6383
• 0 • written 8 weeks ago by
Durian
• 0
2
votes
2
replies
347
views
Identifying differentially expressed genes in individual samples from a large cohort
limma
DifferentialExpression
12 weeks ago
jamie.gearing
▴ 60
0
votes
1
reply
281
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
ilaria.massaiu
• 0
5
votes
13
replies
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 4 months ago by
Gordon Smyth
53k • written 5 months ago by
abaed
• 0
0
votes
4
replies
509
views
voomLmFit fitted log-CPM values
limma
edgeR
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
Lina
▴ 10
1
vote
3
replies
437
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 5 months ago by
Jiahao Tian
• 0
3
votes
4
replies
664
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 4 months ago by
Josh
• 0 • written 6 months ago by
ocanorocabayera
• 0
2
votes
8
replies
840
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 5 months ago by
Gordon Smyth
53k • written 6 months ago by
richardallenfriedmanbrooklyn
▴ 30
1
vote
2
replies
424
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 6 months ago by
A.Barden
▴ 20
1
vote
2
replies
448
views
Difference between logFC in limma-voom and weighted limma-voom
limma
voom
weighting
6 months ago
richardallenfriedmanbrooklyn
▴ 30
3
votes
1
reply
528
views
Limpa Pipeline Order
limma
limpa
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
abadgerw
• 0
3
votes
2
replies
508
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
A.Barden
▴ 20
0
votes
8
replies
740
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
6 months ago
Jiahao Tian
• 0
2
votes
2
replies
501
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago
Basti
▴ 780
2
votes
2
replies
649
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago
sandmann.t
▴ 70
4
votes
8
replies
2.1k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
7 months ago
richardallenfriedmanbrooklyn
▴ 30
7
votes
9
replies
5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
7 months ago
bbao
▴ 10
0
votes
3
replies
2.6k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 7 months ago by
Gordon Smyth
53k • written 7 months ago by
anni
• 0
0
votes
4
replies
1.9k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db
zebrafish
limma
8 months ago
Eric
• 0
3
votes
2
replies
6.5k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago
Geoff
• 0
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
8 months ago
Paulito
• 0
0
votes
1
reply
531
views
Typo in the help of lmFit()
limma
updated 8 months ago by
Gordon Smyth
53k • written 8 months ago by
Balazs
• 0
0
votes
2
replies
1.6k
views
Limma trend with limpa
limpa
limma
trend
updated 8 months ago by
Gordon Smyth
53k • written 8 months ago by
Alejandro
• 0
0
votes
2
replies
748
views
Limma suqeezeVar
limma
8 months ago
Mengchun
• 0
2
votes
5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 9 months ago by
Thomas
• 0
5
votes
7
replies
3.6k
views
limma correction for tumor purity
limma
9 months ago
gabriella.jacobson-eisenberg
▴ 20
4
votes
7
replies
3.6k
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
9 months ago • updated 4 months ago
massimo
▴ 10
0
votes
0
replies
533
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
9 months ago
jamiecatalano2
• 0
2
votes
1
reply
792
views
ROAST for small sets
limma
mroast
updated 9 months ago by
Gordon Smyth
53k • written 9 months ago by
Jiahao Tian
• 0
2
votes
4
replies
2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 months ago by
TraceMorrow
• 0 • written 10 months ago by
matthew
• 0
0
votes
3
replies
1.2k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR
limma
written 10 months ago by
skiaphrene
▴ 10
2
votes
2
replies
1.7k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
robinpaul85
• 0
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA
limma
written 10 months ago by
Jiahao Tian
• 0
5
votes
3
replies
1.4k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 11 months ago by
Gordon Smyth
53k • written 11 months ago by
Devin
▴ 10
2
votes
2
replies
1.8k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
11 months ago
Elizabeth
• 0
1
vote
2
replies
1.3k
views
Differential expression of proteins using somascan data
somascan
limma
written 11 months ago by
kkeole1
• 0
2
votes
4
replies
1.8k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
11 months ago
svlachavas
▴ 840
3
votes
5
replies
2.5k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Jonathan
▴ 10
0
votes
0
replies
438
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
13 months ago
GJ
• 0
0
votes
2
replies
759
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 13 months ago by
svlachavas
▴ 840
2
votes
5
replies
1.0k
views
Differential variability modelling with vst() expression
limma
DESeq2
written 13 months ago by
jtsy6383
• 0
6
votes
5
replies
1.2k
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
1sunmic2
• 0
0
votes
2
replies
887
views
Cross-validation with multiple control subgroups in limma
limma
multtest
13 months ago
Ali Barry
▴ 40
1
vote
9
replies
1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 14 months ago by
anna.cot.anna.cot
▴ 40
0
votes
2
replies
812
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
14 months ago
Tadeoye
▴ 20
0
votes
2
replies
1.0k
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 14 months ago by
Gordon Smyth
53k • written 14 months ago by
Lina
▴ 10
4,231 results • Page
1 of 85
Recent ...
Replies
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
• 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2
by
colinmccornack
• 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Erik Wright
▴ 150
This has to do with the fact that some taxonomies reuse names at the same rank level. Common examples in the SILVA taxonomy are "Incertae S…
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
by
a2a2ddrhaa
• 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]?
by
ATpoint
★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Votes
Answer: Can you colour dendrogram branch clusters in pheatmap?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Awards
• All
Popular Question
to
Peter Hickey
▴ 760
Popular Question
to
Sean Davis
21k
Popular Question
to
James W. MacDonald
68k
Popular Question
to
shepherl
4.3k
Popular Question
to
Andreas Zankl
▴ 80
Locations
• All
The city by the bay,
just now
WEHI, Melbourne, Australia,
8 minutes ago
South Korea,
18 minutes ago
Melbourne, Australia,
1 hour ago
United States,
3 hours ago
Traffic: 2463 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