Showing : LIMMA • reset
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273
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ROAST for small sets
limma mroast
updated 1 day ago by 52k • written 1 day ago by • 0
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3
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1.3k
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how to use `arrayWeightsQuick()`?
limma
updated 13 days ago by 52k • written 14 days ago by • 0
0
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2
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457
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
updated 11 days ago by 52k • written 15 days ago by ▴ 10
2
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2
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1.2k
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 28 days ago by ★ 4.8k • written 29 days ago by • 0
2
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3
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688
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Explanation for ROAST results
CAMERA limma
updated 29 days ago by 52k • written 29 days ago by • 0
5
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3
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833
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 5 weeks ago by 52k • written 5 weeks 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
6 weeks ago • updated 5 weeks ago Elizabeth • 0
1
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2
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842
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Differential expression of proteins using somascan data
somascan limma
written 6 weeks ago by • 0
2
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4
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983
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
9 weeks ago • updated 7 weeks ago svlachavas ▴ 840
3
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5
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1.4k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 3 months ago by 68k • written 3 months ago by ▴ 10
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0
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203
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
3 months ago GJ • 0
0
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2
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497
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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 3 months ago by ▴ 840
2
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5
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513
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Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
6
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5
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757
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 3 months ago by 68k • written 3 months ago by • 0
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2
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574
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Cross-validation with multiple control subgroups in limma
limma multtest
4 months ago Ali Barry ▴ 40
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9
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1.1k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
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2
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435
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
4 months ago Tadeoye ▴ 20
0
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2
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614
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
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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 4 months ago by 68k • written 4 months ago by ▴ 10
1
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2
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530
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contrast matrix design for a continuous variable
limma
4 months ago • updated 3 months ago dtzhu337 • 0
3
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3
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794
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Crossover design with limma
limma crossover
updated 4 months ago by 52k • written 4 months ago by ▴ 30
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9
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1.2k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 4 months ago by • 0
6
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10
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2.9k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 4 months ago by ★ 4.8k • written 4 months ago by ▴ 10
1
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3
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570
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 months ago by • 0
0
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2
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292
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
5 months ago giulia.gentile ▴ 10
4
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2
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764
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 5 months ago by 52k • written 5 months ago by ▴ 60
1
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2
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352
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Limma Interaction Effect with Covariates
limma DMRcate
5 months ago kitzhu • 0
2
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3
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1.1k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 5 months ago by 52k • written 5 months ago by • 0
3
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4
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887
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
5 months ago dseauer • 0
1
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3
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597
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
0
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5
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877
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
1
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8
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1.9k
views
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 Ai • 0
3
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3
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1.2k
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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969
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Analysis of 2*4 factorial design
limma
updated 5 months ago by 52k • written 6 months ago by • 0
2
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12
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2.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
6 months ago • updated 5 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 6 months ago by 52k • written 6 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
6 months ago • updated 5 months ago altintas.ali • 0
2
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2
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572
views
Automatically generate contrasts from a model matrix / formula
limma
updated 6 months ago by ★ 4.8k • written 6 months ago by ▴ 10
3
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3
replies
474
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
0
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3
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565
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Need help interpreting heatmaps from limma
limma
written 6 months ago by • 0
2
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1
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1.8k
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 6 months ago by 68k • written 6 months ago by ▴ 10
5
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4
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739
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
1
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2
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651
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 months ago by 43k • written 7 months ago by ▴ 10
0
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0
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343
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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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558
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 6 months ago by 52k • written 7 months ago by • 0
0
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2
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620
views
Question on performing ANOVA-like analysis using limma
limma
updated 7 months ago by 52k • written 7 months ago by • 0
17
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9
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7.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 months ago by 68k • written 8.9 years ago by ▴ 10
2
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1
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539
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 7 months ago by 68k • written 7 months ago by ▴ 20
0
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1
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1.5k
views
Unable to install/use limma
limma Bioconductor
updated 7 months ago by 68k • written 7 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Comment: RNA Seq using Lrt by Rob • 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Votes
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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