Showing : limma • reset
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ROAST for small sets
limma mroast
updated 2 days ago by 52k • written 3 days ago by • 0
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3
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1.4k
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how to use `arrayWeightsQuick()`?
limma
updated 14 days ago by 52k • written 15 days ago by • 0
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468
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
updated 12 days ago by 52k • written 17 days ago by ▴ 10
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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 4 weeks ago by ★ 4.8k • written 4 weeks ago by • 0
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3
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695
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Explanation for ROAST results
CAMERA limma
updated 4 weeks ago by 52k • written 4 weeks ago by • 0
5
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3
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836
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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
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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
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844
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Differential expression of proteins using somascan data
somascan limma
written 7 weeks ago by • 0
2
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4
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987
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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
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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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205
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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
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2
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498
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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
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5
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516
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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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761
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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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576
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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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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
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2
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617
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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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531
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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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797
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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
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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
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3
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571
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 months ago by • 0
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2
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293
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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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769
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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
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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
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[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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892
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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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598
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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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882
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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
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
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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
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1.2k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
4
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3
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971
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Analysis of 2*4 factorial design
limma
updated 5 months ago by 52k • written 6 months ago by • 0
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12
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2.2k
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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 altintas.ali • 0
2
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2
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574
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
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479
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
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3
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571
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Need help interpreting heatmaps from limma
limma
written 6 months ago by • 0
2
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1.8k
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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
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4
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740
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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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653
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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345
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
7 months ago • updated 6 months ago tim.meese • 0
0
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2
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561
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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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621
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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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541
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
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Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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