Showing : limma • reset
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133
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Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
updated 5 days ago by 53k • written 6 days ago by • 0
4
votes
2
replies
316
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Limma-voom sample weights and impact on DEG numbers
limma
21 days ago • updated 8 days ago A.Barden ▴ 20
0
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4
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568
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 8 days ago by • 0 • written 26 days ago by • 0
0
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1
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1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 6 weeks ago by 53k • written 18.9 years ago by ▴ 240
2
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2
replies
307
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
8 weeks ago • updated 7 weeks ago jamie.gearing ▴ 60
1
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2
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391
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
0
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1
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247
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
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13
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1.4k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 3 months ago by 53k • written 4 months ago by • 0
0
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4
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474
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
1
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3
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402
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ROAST compare results with complex design
limma mroast roast CAMERA
written 4 months ago by • 0
2
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8
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788
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 4 months ago by 53k • written 5 months ago by ▴ 30
3
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4
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595
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 3 months ago by • 0 • written 5 months ago by • 0
1
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2
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415
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
5 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
429
views
Limpa Pipeline Order
limma limpa
updated 5 months ago by 53k • written 5 months ago by • 0
3
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2
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484
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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
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8
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686
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 months ago Jiahao Tian • 0
2
votes
2
replies
454
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Limma : paired samples leading to unexpected estimates
limma
5 months ago Basti ▴ 780
2
votes
2
replies
560
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
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.8k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
0
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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
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3
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2.5k
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
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4
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1.8k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
7 months ago Eric • 0
3
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2
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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
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1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 months ago Paulito • 0
0
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1
reply
508
views
Typo in the help of lmFit()
limma
updated 7 months ago by 53k • written 7 months ago by • 0
0
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2
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704
views
Limma suqeezeVar
limma
7 months ago Mengchun • 0
0
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2
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1.4k
views
Limma trend with limpa
limpa limma trend
updated 7 months ago by 53k • written 7 months ago by • 0
2
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5
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1.3k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 8 months ago by • 0
5
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7
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3.5k
views
limma correction for tumor purity
limma
8 months ago gabriella.jacobson-eisenberg ▴ 20
0
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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
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7
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3.4k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
8 months ago • updated 3 months ago massimo ▴ 10
0
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0
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492
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
8 months ago jamiecatalano2 • 0
2
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1
reply
747
views
ROAST for small sets
limma mroast
updated 8 months ago by 53k • written 8 months ago by • 0
2
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4
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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
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4
replies
1.0k
views
Explanation for ROAST results
CAMERA limma
written 9 months ago by • 0
5
votes
3
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1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 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 Elizabeth • 0
1
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2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan limma
written 10 months ago by • 0
2
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4
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1.6k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
10 months ago svlachavas ▴ 840
3
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5
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2.3k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
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0
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408
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
12 months ago GJ • 0
0
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2
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709
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
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5
replies
930
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
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2
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848
views
Cross-validation with multiple control subgroups in limma
limma multtest
12 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 13 months ago by ▴ 40
0
votes
2
replies
772
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
989
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
4,229 results • Page 1 of 85
Recent ...
Replies
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
@mikelove Could I please ask if a similar method would work my set of samples? I have 255 samples which have been generated from 76 subject…
Comment: Clarification on counting in Rsubread (featureCounts) by Luca • 0
Thanks to both of you for your helpful suggestions. The counting was already strand-specific at both the exon and gene levels. I resolved …
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Lluís Revilla Sancho ▴ 760
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Gordon Smyth 53k
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