Showing : LIMMA • reset
4
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2
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272
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When to use edgeR or limma
edgeR limma
updated 10 days ago by 53k • written 13 days ago by • 0
0
votes
2
replies
282
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
19 days ago • updated 5 days ago Andrew Pattison • 0
4
votes
2
replies
421
views
Limma-voom sample weights and impact on DEG numbers
limma
4 weeks ago • updated 22 days ago A.Barden ▴ 20
0
votes
4
replies
609
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 21 days ago by • 0 • written 5 weeks ago by • 0
0
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1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 8 weeks ago by 53k • written 18.9 years ago by ▴ 240
2
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2
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317
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
10 weeks ago • updated 9 weeks ago jamie.gearing ▴ 60
1
vote
2
replies
407
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
0
votes
1
reply
259
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
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1.5k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 4 months ago by • 0
0
votes
4
replies
490
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
1
vote
3
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413
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 4 months ago by • 0
2
votes
8
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807
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 4 months ago by 53k • written 5 months ago by ▴ 30
3
votes
4
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627
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
428
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
5 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
462
views
Limpa Pipeline Order
limma limpa
updated 5 months ago by 53k • written 5 months ago by • 0
3
votes
2
replies
492
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
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709
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 months ago Jiahao Tian • 0
2
votes
2
replies
475
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
599
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
2.0k
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
votes
9
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5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
0
votes
1
reply
1.5k
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 17.0 years ago by ▴ 10
0
votes
3
replies
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
1.9k
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
votes
2
replies
6.4k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago • updated 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
8 months ago Paulito • 0
0
votes
1
reply
518
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
0
votes
2
replies
721
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
0
votes
2
replies
1.5k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 8 months ago by • 0
2
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5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 8 months ago by • 0
5
votes
7
replies
3.5k
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
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7
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3.5k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 3 months ago massimo ▴ 10
0
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0
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506
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
761
views
ROAST for small sets
limma mroast
updated 9 months ago by 53k • written 9 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 10 months ago by ★ 5.0k • written 10 months ago by • 0
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 10 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
2
replies
1.2k
views
Differential expression of proteins using somascan data
somascan limma
written 10 months ago by • 0
2
votes
4
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1.6k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
11 months ago • updated 10 months ago svlachavas ▴ 840
3
votes
5
replies
2.4k
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
votes
0
replies
416
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
votes
2
replies
731
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
971
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 months ago by • 0
6
votes
5
replies
1.2k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 12 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
862
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 13 months ago by ▴ 40
0
votes
2
replies
785
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
13 months ago Tadeoye ▴ 20
4,230 results • Page 1 of 85
Recent ...
Replies
Answer: lfc shrinkage estimator in DESeq2 by plumsgorillas • 0
You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. However,…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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