Showing : limma • reset
4
votes
2
replies
232
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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 • 0 • written 19 days ago by • 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 5 weeks ago by 53k • written 18.9 years ago by ▴ 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 ▴ 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 53k • written 3 months ago by • 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 53k • written 3 months ago by • 0
0
votes
4
replies
467
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
1
vote
3
replies
394
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 4 months ago by • 0
2
votes
8
replies
784
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 4 months ago by 53k • written 4 months ago by ▴ 30
3
votes
4
replies
584
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 3 months ago by • 0 • written 4 months ago by • 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 53k • written 5 months ago by • 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 53k • written 5 months ago by ▴ 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 53k • written 16.9 years ago by ▴ 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 53k • written 6 months ago by • 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 53k • written 7 months ago by • 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 53k • written 7 months ago by • 0
2
votes
5
replies
1.3k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 8 months ago by • 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 ▴ 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
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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 53k • written 8 months ago by • 0
2
votes
4
replies
2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 8 months ago by • 0 • written 9 months ago by • 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 ★ 5.0k • written 9 months ago by • 0
2
votes
4
replies
1.0k
views
Explanation for ROAST results
CAMERA limma
written 9 months ago by • 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 53k • written 9 months ago by ▴ 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 • 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 68k • written 11 months ago by ▴ 10
0
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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 ▴ 840
2
votes
5
replies
895
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 months ago by • 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 68k • written 12 months ago by • 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 ▴ 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 53k • written 13 months ago by ▴ 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 68k • written 13 months ago by ▴ 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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