Showing : Limma • reset
1
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283
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 12 weeks ago by ▴ 10
0
votes
1
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163
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 weeks ago by 53k • written 5 weeks ago by • 0
5
votes
13
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1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 6 weeks ago by 53k • written 8 weeks ago by • 0
0
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4
replies
400
views
voomLmFit fitted log-CPM values
limma edgeR
updated 8 weeks ago by 53k • written 9 weeks ago by ▴ 10
1
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3
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338
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 9 weeks ago by • 0
2
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8
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684
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 9 weeks ago by 53k • written 11 weeks ago by ▴ 30
3
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4
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475
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 7 weeks ago by • 0 • written 11 weeks ago by • 0
1
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2
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336
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
3 months ago • updated 12 weeks ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
321
views
Limpa Pipeline Order
limma limpa
updated 3 months ago by 53k • written 3 months ago by • 0
3
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2
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418
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Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 3 months ago by 53k • written 3 months ago by ▴ 10
0
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8
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590
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago Jiahao Tian • 0
2
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2
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387
views
Limma : paired samples leading to unexpected estimates
limma
3 months ago Basti ▴ 780
2
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2
replies
437
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
3 months ago sandmann.t ▴ 70
4
votes
8
replies
1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
7
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9
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5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
0
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1
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1.4k
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How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 3 months ago by 53k • written 16.8 years ago by ▴ 10
0
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3
replies
2.3k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 4 months ago by 53k • written 4 months ago by • 0
0
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4
replies
1.7k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
4 months ago Eric • 0
3
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2
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6.3k
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limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
5 months ago Geoff • 0
2
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3
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1.4k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago Paulito • 0
0
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1
reply
463
views
Typo in the help of lmFit()
limma
updated 5 months ago by 53k • written 5 months ago by • 0
0
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2
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646
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Limma suqeezeVar
limma
5 months ago Mengchun • 0
0
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2
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756
views
Limma trend with limpa
limpa limma trend
updated 5 months ago by 53k • written 5 months ago by • 0
2
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5
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1.2k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 6 months ago by • 0
5
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7
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3.3k
views
limma correction for tumor purity
limma
6 months ago • updated 5 months ago gabriella.jacobson-eisenberg ▴ 20
0
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3
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961
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 7 months ago by ▴ 10
4
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7
replies
3.3k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
6 months ago • updated 4 weeks ago massimo ▴ 10
0
votes
0
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431
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
6 months ago jamiecatalano2 • 0
2
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1
reply
667
views
ROAST for small sets
limma mroast
updated 6 months ago by 53k • written 6 months ago by • 0
2
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4
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1.8k
views
how to use `arrayWeightsQuick()`?
limma
updated 6 months ago by • 0 • written 7 months ago by • 0
2
votes
2
replies
1.5k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
2
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4
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953
views
Explanation for ROAST results
CAMERA limma
written 7 months ago by • 0
5
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3
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1.2k
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 7 months ago by 53k • written 7 months ago by ▴ 10
2
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2
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1.5k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
8 months ago • updated 7 months ago Elizabeth • 0
1
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2
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1.0k
views
Differential expression of proteins using somascan data
somascan limma
written 8 months ago by • 0
2
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4
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1.4k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
8 months ago svlachavas ▴ 840
3
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5
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2.0k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 months ago by 68k • written 9 months ago by ▴ 10
0
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0
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367
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 months ago GJ • 0
0
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2
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646
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 10 months ago by ▴ 840
2
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5
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772
views
Differential variability modelling with vst() expression
limma DESeq2
written 10 months ago by • 0
6
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5
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1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 10 months ago by 68k • written 10 months ago by • 0
0
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2
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778
views
Cross-validation with multiple control subgroups in limma
limma multtest
10 months ago Ali Barry ▴ 40
1
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9
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1.5k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 10 months ago by ▴ 40
0
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2
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695
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 months ago Tadeoye ▴ 20
0
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2
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875
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 11 months ago by 53k • written 11 months ago by ▴ 10
2
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3
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1.7k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 11 months ago by 68k • written 11 months ago by ▴ 10
1
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2
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702
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contrast matrix design for a continuous variable
limma
11 months ago • updated 9 months ago dtzhu337 • 0
3
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3
replies
1.0k
views
Crossover design with limma
limma crossover
updated 10 months ago by 53k • written 11 months ago by ▴ 30
0
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9
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1.7k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 months ago by 68k • written 11 months ago by • 0
6
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10
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3.3k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 11 months ago by ★ 5.0k • written 11 months ago by ▴ 10
4,225 results • Page 1 of 85
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Replies
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors by James W. MacDonald 68k
Note that `S4Vectors` contains source code, so you will also need to [install RTools first][1]. [1]: https://cran.r-project.org/bin/win…
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors by shepherl 4.2k
Our windows binaries are currently lagging behind as we are currently do not have a windows builder. If you are on windows you can try ins…
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors by shepherl 4.2k
Can you please provide your `sessionInfo()` after doing `library("S4Vectors")`
Comment: VariantAnnotation does escape = within header string quotes by Daniel Cameron ▴ 40
I'm just stripping the entire line as a workaround using `meta(header(vcf))$DRAGENCommandLine = NULL`. Not ideal but at least subsequent pa…
Comment: Setting up a DESeq2 Design with Paired Data by Alexander • 0
Hi Kevin, Firstly, thank you so much for not only a very prompt response, but one that is incredibly insightful and helps me learn DESeq2 …
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
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Popular Question to edward.esiribloom • 0
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