Showing : limma • reset
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 8 days ago by ★ 4.8k • written 9 days ago by • 0
2
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3
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640
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Explanation for ROAST results
CAMERA limma
updated 8 days ago by 52k • written 9 days ago by • 0
5
votes
3
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770
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 15 days ago by 52k • written 16 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
23 days ago • updated 17 days ago Elizabeth • 0
1
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2
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784
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Differential expression of proteins using somascan data
somascan limma
written 27 days ago by • 0
2
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4
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924
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
6 weeks ago • updated 4 weeks ago svlachavas ▴ 840
3
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5
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1.3k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by ▴ 10
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0
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183
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
11 weeks ago GJ • 0
0
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2
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463
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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 11 weeks ago by ▴ 840
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5
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465
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Differential variability modelling with vst() expression
limma DESeq2
written 12 weeks ago by • 0
6
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5
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718
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 12 weeks ago by 68k • written 3 months ago by • 0
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2
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548
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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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999
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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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405
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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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584
views
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
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How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 3 months ago by 68k • written 4 months ago by ▴ 10
1
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2
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509
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contrast matrix design for a continuous variable
limma
4 months ago • updated 10 weeks ago dtzhu337 • 0
3
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3
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758
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Crossover design with limma
limma crossover
updated 3 months ago by 52k • written 4 months ago by ▴ 30
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9
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1.2k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 3 months ago by 68k • written 4 months ago by • 0
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 4 months ago by ▴ 10
1
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3
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542
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 4 months ago by • 0
0
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2
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276
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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
4
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2
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713
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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 ▴ 60
1
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2
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320
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Limma Interaction Effect with Covariates
limma DMRcate
4 months ago kitzhu • 0
2
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3
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1.0k
views
[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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841
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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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572
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
4 months ago abadgerw • 0
0
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5
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844
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
4 months ago abadgerw • 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 5 months ago by • 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
5 months ago • updated 4 months ago Ai • 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
4
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3
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943
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Analysis of 2*4 factorial design
limma
updated 5 months ago by 52k • written 5 months ago by • 0
2
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12
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2.1k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
5 months ago • updated 4 months ago john • 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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530
views
Automatically generate contrasts from a model matrix / formula
limma
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
3
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3
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447
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
0
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3
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539
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Need help interpreting heatmaps from limma
limma
written 5 months ago by • 0
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
replies
678
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 months ago by ★ 4.8k • written 6 months ago by • 0
1
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2
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617
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 6 months ago by ▴ 10
0
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0
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316
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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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524
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 6 months ago by 52k • written 6 months ago by • 0
0
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2
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593
views
Question on performing ANOVA-like analysis using limma
limma
updated 6 months ago by 52k • written 6 months ago by • 0
17
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9
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7.5k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 6 months ago by 68k • written 8.8 years ago by ▴ 10
2
votes
1
reply
497
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 ▴ 20
0
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1
reply
1.3k
views
Unable to install/use limma
limma Bioconductor
updated 7 months ago by 68k • written 7 months ago by • 0
3
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3
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723
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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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1.1k
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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677
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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
50 results • Page 1 of 1
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Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Comment: Question on displaying color photo as Greyscale in EBImage by Albert • 0
great and very nice
Comment: European Bioconductor Conference 2023 planning by Pandora • 0
The [Tag Game][1] is not just a simple chase; it involves strategy and tactics as players must think quickly to avoid being tagged. Various…
Comment: Generalized edgeR functions by bukarimanches • 0
I have estimated the new parameter set, it doesn't seem as useful as I thought [geometry dash lite][1] [1]: https://geometry-lite.com/
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Morse • 0
[Geometry Dash Lite][1] is the free version of the famous Geometry Dash series. It was made by RobTop Games and lets players enjoy the thri…
Votes
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
what the test method for enrichGO in clusterProfiler?
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