Showing : LIMMA • reset
2
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5
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 4 days ago by 67k • written 4 days ago by ▴ 10
0
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0
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62
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
7 days ago GJ • 0
0
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2
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347
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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 days ago by ▴ 840
2
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5
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285
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Differential variability modelling with vst() expression
limma DESeq2
written 11 days ago by • 0
6
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5
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526
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 13 days ago by 67k • written 19 days ago by • 0
0
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2
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447
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Cross-validation with multiple control subgroups in limma
limma multtest
4 weeks ago Ali Barry ▴ 40
1
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9
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801
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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 weeks ago by ▴ 30
0
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2
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307
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
6 weeks ago • updated 5 weeks ago Tadeoye ▴ 20
0
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2
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483
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 6 weeks ago by 52k • written 6 weeks ago by ▴ 10
2
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3
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1.2k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 6 weeks ago by 67k • written 6 weeks ago by ▴ 10
1
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2
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393
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contrast matrix design for a continuous variable
limma
7 weeks ago • updated 13 hours ago dtzhu337 • 0
3
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3
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629
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Crossover design with limma
limma crossover
updated 5 weeks ago by 52k • written 7 weeks ago by ▴ 30
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9
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913
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
6
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10
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2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by ▴ 10
1
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3
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445
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 8 weeks ago by • 0
0
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2
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208
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
9 weeks ago • updated 8 weeks ago giulia.gentile ▴ 10
4
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2
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573
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 9 weeks ago by 52k • written 9 weeks ago by ▴ 50
1
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2
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230
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Limma Interaction Effect with Covariates
limma DMRcate
9 weeks ago kitzhu • 0
2
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3
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911
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[How to construct a model.matrix ]
limma modelmatrix
updated 9 weeks ago by 52k • written 9 weeks ago by • 0
3
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4
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668
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
9 weeks ago dseauer • 0
1
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3
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471
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 7 weeks ago abadgerw • 0
0
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5
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683
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 7 weeks ago abadgerw • 0
1
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8
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1.2k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 weeks ago by • 0
1
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2
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966
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
11 weeks ago • updated 10 weeks ago Ai • 0
3
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3
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947
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 weeks ago by • 0
4
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3
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829
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Analysis of 2*4 factorial design
limma
updated 11 weeks ago by 52k • written 12 weeks ago by • 0
2
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12
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1.7k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
12 weeks ago • updated 8 weeks ago john • 0
4
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6
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1.5k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 3 months ago by 52k • written 3 months ago by • 0
4
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6
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1.2k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
3 months ago • updated 12 weeks ago altintas.ali • 0
2
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2
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378
views
Automatically generate contrasts from a model matrix / formula
limma
updated 3 months ago by ★ 4.6k • written 3 months ago by ▴ 10
3
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3
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343
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
3 months ago Guido Hooiveld ★ 4.1k
0
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3
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399
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Need help interpreting heatmaps from limma
limma
written 3 months ago by • 0
2
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1
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1.5k
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 3 months ago by 67k • written 3 months ago by ▴ 10
5
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4
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522
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
1
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2
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511
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 4 months ago by ▴ 10
0
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0
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258
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
3 months ago tim.meese • 0
0
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2
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414
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 3 months ago by 52k • written 3 months ago by • 0
0
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2
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493
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Question on performing ANOVA-like analysis using limma
limma
updated 4 months ago by 52k • written 4 months ago by • 0
17
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9
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7.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 4 months ago by 67k • written 8.6 years ago by ▴ 10
2
votes
1
reply
387
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 4 months ago by 67k • written 4 months ago by ▴ 10
0
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1
reply
770
views
Unable to install/use limma
limma Bioconductor
updated 4 months ago by 67k • written 4 months ago by • 0
3
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3
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575
views
voom does not seem to properly correct for library size
limma
updated 4 months ago by 52k • written 4 months ago by ★ 4.6k
1
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5
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867
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 4 months ago by 52k • written 5 months ago by • 0
0
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3
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592
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 5 months ago by 52k • written 5 months ago by • 0
3
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4
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671
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using limma trend workflow in CAMERA
CAMERA limma
5 months ago • updated 4 months ago Jay • 0
3
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3
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612
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 5 months ago by 52k • written 5 months ago by ▴ 10
1
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6
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751
views
limma and Syntactically Invalid Factor Values
limma
updated 6 months ago by 52k • written 6 months ago by ★ 1.5k
1
vote
1
reply
638
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
6 months ago Bioinformagician • 0
4
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3
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623
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Limma comparing gene expression between base line and one treatment
limma
updated 6 months ago by 67k • written 6 months ago by • 0
0
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1
reply
602
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 6 months ago by ★ 4.6k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19) by ja.garcia • 0
It has been fixed by the Rbowtie2 maintainers in version 2.12.2. Thank you for the quick fix!
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by Amora • 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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