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Showing :
limma
•
reset
4
votes
2
replies
232
views
Limma-voom sample weights and impact on DEG numbers
limma
15 days ago • updated 2 days ago
A.Barden
▴ 20
0
votes
4
replies
438
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 1 day ago by
jtsy6383
• 0 • written 19 days ago by
Durian
• 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray
limma
Microarray
limma
updated 5 weeks ago by
Gordon Smyth
53k • written 18.9 years ago by
De-Jian ZHAO
▴ 240
2
votes
2
replies
297
views
Identifying differentially expressed genes in individual samples from a large cohort
limma
DifferentialExpression
7 weeks ago
jamie.gearing
▴ 60
1
vote
2
replies
381
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 4 months ago by
A.Barden
▴ 20
0
votes
1
reply
239
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
ilaria.massaiu
• 0
5
votes
13
replies
1.4k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 3 months ago by
Gordon Smyth
53k • written 3 months ago by
abaed
• 0
0
votes
4
replies
467
views
voomLmFit fitted log-CPM values
limma
edgeR
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
Lina
▴ 10
1
vote
3
replies
394
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 4 months ago by
Jiahao Tian
• 0
2
votes
8
replies
784
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
richardallenfriedmanbrooklyn
▴ 30
3
votes
4
replies
584
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 3 months ago by
Josh
• 0 • written 4 months ago by
ocanorocabayera
• 0
1
vote
2
replies
408
views
Difference between logFC in limma-voom and weighted limma-voom
limma
voom
weighting
5 months ago • updated 4 months ago
richardallenfriedmanbrooklyn
▴ 30
3
votes
1
reply
417
views
Limpa Pipeline Order
limma
limpa
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
abadgerw
• 0
3
votes
2
replies
481
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
A.Barden
▴ 20
0
votes
8
replies
682
views
How to use limma to analyze complex temporal RNAseq data
timecourse
RNASeq
limma
5 months ago
Jiahao Tian
• 0
2
votes
2
replies
449
views
Limma : paired samples leading to unexpected estimates
limma
5 months ago
Basti
▴ 780
2
votes
2
replies
553
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
5 months ago
sandmann.t
▴ 70
4
votes
8
replies
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2
edgeR
limma
xenium
Voom
5 months ago
richardallenfriedmanbrooklyn
▴ 30
7
votes
9
replies
5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma
DESeq2
fry
edgeR
5 months ago
bbao
▴ 10
0
votes
1
reply
1.4k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray
limma
BRAIN
Microarray
limma
BRAIN
updated 6 months ago by
Gordon Smyth
53k • written 16.9 years ago by
Dmitriy Verkhoturov
▴ 10
0
votes
3
replies
2.4k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma
Bioconductor
Metabolomics
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
anni
• 0
0
votes
4
replies
1.8k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db
zebrafish
limma
6 months ago
Eric
• 0
3
votes
2
replies
6.4k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
7 months ago
Geoff
• 0
2
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
7 months ago
Paulito
• 0
0
votes
1
reply
503
views
Typo in the help of lmFit()
limma
updated 7 months ago by
Gordon Smyth
53k • written 7 months ago by
Balazs
• 0
0
votes
2
replies
695
views
Limma suqeezeVar
limma
7 months ago
Mengchun
• 0
0
votes
2
replies
1.4k
views
Limma trend with limpa
limpa
limma
trend
updated 7 months ago by
Gordon Smyth
53k • written 7 months ago by
Alejandro
• 0
2
votes
5
replies
1.3k
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 8 months ago by
Thomas
• 0
5
votes
7
replies
3.4k
views
limma correction for tumor purity
limma
8 months ago
gabriella.jacobson-eisenberg
▴ 20
0
votes
3
replies
1.1k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR
limma
written 9 months ago by
skiaphrene
▴ 10
4
votes
7
replies
3.4k
views
Check removeBatchEffect effectiveness
RNAseq
limma
removeBatchEffect
8 months ago • updated 3 months ago
massimo
▴ 10
0
votes
0
replies
489
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
8 months ago
jamiecatalano2
• 0
2
votes
1
reply
742
views
ROAST for small sets
limma
mroast
updated 8 months ago by
Gordon Smyth
53k • written 8 months ago by
Jiahao Tian
• 0
2
votes
4
replies
2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 8 months ago by
TraceMorrow
• 0 • written 9 months ago by
matthew
• 0
2
votes
2
replies
1.6k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR
limma
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
robinpaul85
• 0
2
votes
4
replies
1.0k
views
Explanation for ROAST results
CAMERA
limma
written 9 months ago by
Jiahao Tian
• 0
5
votes
3
replies
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR
limma
voomLmFit
updated 9 months ago by
Gordon Smyth
53k • written 9 months ago by
Devin
▴ 10
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR
contrastmatrix
limma
10 months ago • updated 9 months ago
Elizabeth
• 0
1
vote
2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan
limma
written 10 months ago by
kkeole1
• 0
2
votes
4
replies
1.6k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis
limma
olinktargetedproteomics
10 months ago
svlachavas
▴ 840
3
votes
5
replies
2.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma
edgeR
biomaRt
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Jonathan
▴ 10
0
votes
0
replies
403
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
11 months ago
GJ
• 0
0
votes
2
replies
701
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 12 months ago by
svlachavas
▴ 840
2
votes
5
replies
895
views
Differential variability modelling with vst() expression
limma
DESeq2
written 12 months ago by
jtsy6383
• 0
6
votes
5
replies
1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma
Normalization
voom
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
1sunmic2
• 0
0
votes
2
replies
839
views
Cross-validation with multiple control subgroups in limma
limma
multtest
12 months ago
Ali Barry
▴ 40
1
vote
9
replies
1.6k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 12 months ago by
anna.cot.anna.cot
▴ 40
0
votes
2
replies
763
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
13 months ago
Tadeoye
▴ 20
0
votes
2
replies
975
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Lina
▴ 10
2
votes
3
replies
1.9k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
giulia.gentile
▴ 10
4,228 results • Page
1 of 85
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
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