Showing : Limma • reset
4
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2
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146
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When to use edgeR or limma
edgeR limma
updated 1 day ago by 53k • written 4 days ago by • 0
0
votes
1
reply
166
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
updated 10 days ago by 53k • written 10 days ago by • 0
0
votes
4
replies
584
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 12 days ago by • 0 • written 4 weeks ago by • 0
4
votes
2
replies
365
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Limma-voom sample weights and impact on DEG numbers
limma
26 days ago • updated 13 days ago A.Barden ▴ 20
0
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1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 7 weeks ago by 53k • written 18.9 years ago by ▴ 240
0
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2
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1.7k
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how does limma calculate the coefficients with using different design matrix?
probe limma
15.4 years ago • updated 7 weeks ago Gordon Smyth 53k
0
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2
replies
1.3k
views
missing values in limma/contrasts.fit
Microarray limma Regression probe
16.1 years ago • updated 7 weeks ago Gordon Smyth 53k
2
votes
2
replies
313
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
8 weeks ago jamie.gearing ▴ 60
1
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2
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395
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
4
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7
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3.5k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
8 months ago • updated 3 months ago massimo ▴ 10
0
votes
1
reply
249
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
1
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1
reply
1.1k
views
ordinary t from limma [was: How would I normally compare swirl?]
GO limma Bioconductor
21.6 years ago • updated 3 months ago Gordon Smyth 53k
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 4 months ago by • 0
3
votes
4
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608
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 5 months ago by • 0
0
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4
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478
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
2
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4
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1.0k
views
Explanation for ROAST results
CAMERA limma
written 9 months ago by • 0
1
vote
3
replies
404
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 4 months ago by • 0
2
votes
8
replies
792
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 4 months ago by 53k • written 5 months ago by ▴ 30
1
vote
2
replies
418
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
5 months ago richardallenfriedmanbrooklyn ▴ 30
0
votes
8
replies
690
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 months ago Jiahao Tian • 0
3
votes
2
replies
486
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
3
votes
1
reply
445
views
Limpa Pipeline Order
limma limpa
updated 5 months ago by 53k • written 5 months ago by • 0
0
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5
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7.7k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R Pathways pheatmap limma
written 4.8 years ago by ▴ 10
2
votes
2
replies
460
views
Limma : paired samples leading to unexpected estimates
limma
5 months ago Basti ▴ 780
2
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2
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572
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(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
5 months ago sandmann.t ▴ 70
2
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15
replies
4.4k
views
Annotation of Affy Porcine Gene 1.0 ST array data
limma oligo annotation
updated 5 months ago by • 0 • written 11.0 years ago by • 0
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
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
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
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0
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1.1k
views
Re: LIMMA normalizeForPrintorder
BRAIN Normalization limma ASSIGN
22.6 years ago • updated 6 months ago Gordon Smyth 53k
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
votes
4
replies
1.8k
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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
replies
6.4k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
7 months ago Geoff • 0
12
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5
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5.3k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by • 0 • written 2.1 years ago by • 0
0
votes
2
replies
1.4k
views
Limma trend with limpa
limpa limma trend
updated 7 months ago by 53k • written 8 months ago by • 0
2
votes
3
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1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago • updated 7 months ago Paulito • 0
0
votes
2
replies
710
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
0
votes
1
reply
510
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
5
votes
7
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3.5k
views
limma correction for tumor purity
limma
8 months ago gabriella.jacobson-eisenberg ▴ 20
2
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5
replies
1.3k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 8 months ago by • 0
0
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3
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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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0
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3.4k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray Normalization Bayesian Regression Cancer limma Microarray Normalization Cancer
updated 8 months ago by • 0 • written 14.7 years ago by ★ 2.0k
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
0
votes
0
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494
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
751
views
ROAST for small sets
limma mroast
updated 9 months ago by 53k • written 9 months ago by • 0
0
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3
replies
2.3k
views
RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
written 22.0 years ago by ▴ 70
2
votes
2
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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
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 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
vote
8
replies
2.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
4,230 results • Page 1 of 85
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Comment: Are individual-mouse-based statistics possible in CellChat? by TikTsossakaas33ocissalpc • 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
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.
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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