Showing : Limma • reset
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 23 hours ago by ★ 4.8k • written 1 day ago by • 0
1
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3
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231
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Explanation for ROAST results
CAMERA limma
updated 1 day ago by 52k • written 1 day ago by • 0
5
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3
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745
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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 days ago by 52k • written 8 days ago by ▴ 10
2
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2
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1.1k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
15 days ago • updated 10 days ago Elizabeth • 0
1
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2
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761
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Differential expression of proteins using somascan data
somascan limma
written 19 days ago by • 0
2
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4
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896
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
5 weeks ago • updated 23 days ago svlachavas ▴ 840
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5
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1.2k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by ▴ 10
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0
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182
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
10 weeks ago GJ • 0
0
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2
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455
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Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 10 weeks ago by ▴ 840
2
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5
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446
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Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
6
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5
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687
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
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2
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545
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Cross-validation with multiple control subgroups in limma
limma multtest
3 months ago Ali Barry ▴ 40
1
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9
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978
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
0
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2
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401
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
3 months ago Tadeoye ▴ 20
0
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2
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575
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
2
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3
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1.4k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 3 months ago by 68k • written 3 months ago by ▴ 10
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2
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497
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contrast matrix design for a continuous variable
limma
3 months ago • updated 9 weeks ago dtzhu337 • 0
0
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9
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1.1k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 3 months ago by 68k • written 3 months ago by • 0
3
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3
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735
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Crossover design with limma
limma crossover
updated 3 months ago by 52k • written 3 months ago by ▴ 30
6
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10
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2.8k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
1
vote
3
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531
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 4 months ago by • 0
1
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2
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315
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Limma Interaction Effect with Covariates
limma DMRcate
4 months ago kitzhu • 0
4
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2
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698
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 4 months ago by 52k • written 4 months ago by ▴ 50
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2
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273
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
4 months ago giulia.gentile ▴ 10
2
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3
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1.0k
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[How to construct a model.matrix ]
limma modelmatrix
updated 4 months ago by 52k • written 4 months ago by • 0
3
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4
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823
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
4 months ago dseauer • 0
1
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3
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557
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
0
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5
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816
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
1
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2
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1.1k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
4 months ago Ai • 0
1
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8
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1.7k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
3
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3
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1.1k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 months ago by • 0
2
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12
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2.1k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
5 months ago • updated 4 months ago john • 0
4
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3
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922
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Analysis of 2*4 factorial design
limma
updated 4 months ago by 52k • written 5 months ago by • 0
4
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6
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1.7k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 5 months ago by 52k • written 5 months ago by • 0
4
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6
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1.4k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago altintas.ali • 0
2
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2
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522
views
Automatically generate contrasts from a model matrix / formula
limma
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
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3
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527
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Need help interpreting heatmaps from limma
limma
written 5 months ago by • 0
3
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3
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439
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
2
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1
reply
1.7k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 5 months ago by 68k • written 5 months ago by ▴ 10
5
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4
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667
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
0
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0
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308
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
6 months ago tim.meese • 0
0
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2
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513
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 6 months ago by • 0
1
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2
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608
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 6 months ago by ▴ 10
0
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2
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578
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Question on performing ANOVA-like analysis using limma
limma
updated 6 months ago by 52k • written 6 months ago by • 0
2
votes
1
reply
478
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 6 months ago by 68k • written 6 months ago by ▴ 10
0
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1
reply
1.3k
views
Unable to install/use limma
limma Bioconductor
updated 6 months ago by 68k • written 6 months ago by • 0
3
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3
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707
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voom does not seem to properly correct for library size
limma
updated 7 months ago by 52k • written 7 months ago by ★ 4.8k
1
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5
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1.0k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 7 months ago by 52k • written 7 months ago by • 0
0
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3
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671
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 7 months ago by 52k • written 7 months ago by • 0
3
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4
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815
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using limma trend workflow in CAMERA
CAMERA limma
7 months ago Jay • 0
50 results • Page 1 of 1
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
What is the cheapest day to fly on American Airlines? {Ask_Expert}
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