Showing : Limma • reset
2
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1.3k
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how to use `arrayWeightsQuick()`?
limma
updated 9 days ago by 52k • written 11 days ago by • 0
0
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2
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444
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
updated 7 days ago by 52k • written 12 days ago by ▴ 10
2
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2
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1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 25 days ago by ★ 4.8k • written 26 days ago by • 0
2
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3
replies
680
views
Explanation for ROAST results
CAMERA limma
updated 25 days ago by 52k • written 26 days ago by • 0
5
votes
3
replies
825
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 4 weeks ago by 52k • written 4 weeks ago by ▴ 10
2
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2
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1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
5 weeks ago • updated 4 weeks ago Elizabeth • 0
1
vote
2
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831
views
Differential expression of proteins using somascan data
somascan limma
written 6 weeks ago by • 0
2
votes
4
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965
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
8 weeks ago • updated 6 weeks ago svlachavas ▴ 840
3
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5
replies
1.4k
views
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
0
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0
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199
views
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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493
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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
replies
504
views
Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
6
votes
5
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751
views
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
0
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2
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567
views
Cross-validation with multiple control subgroups in limma
limma multtest
4 months ago Ali Barry ▴ 40
1
vote
9
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1.1k
views
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
0
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2
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428
views
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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610
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
2
votes
3
replies
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
vote
2
replies
524
views
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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785
views
Crossover design with limma
limma crossover
updated 4 months ago by 52k • written 4 months ago by ▴ 30
0
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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
votes
10
replies
2.9k
views
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
vote
3
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565
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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290
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
5 months ago giulia.gentile ▴ 10
4
votes
2
replies
753
views
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
vote
2
replies
340
views
Limma Interaction Effect with Covariates
limma DMRcate
5 months ago kitzhu • 0
2
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3
replies
1.1k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 5 months ago by 52k • written 5 months ago by • 0
3
votes
4
replies
882
views
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
replies
590
views
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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872
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
1
vote
8
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1.8k
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
replies
1.1k
views
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
votes
3
replies
964
views
Analysis of 2*4 factorial design
limma
updated 5 months ago by 52k • written 5 months ago by • 0
2
votes
12
replies
2.2k
views
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
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 5 months ago by 52k • written 6 months ago by • 0
4
votes
6
replies
1.4k
views
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
votes
2
replies
562
views
Automatically generate contrasts from a model matrix / formula
limma
updated 6 months ago by ★ 4.8k • written 6 months ago by ▴ 10
3
votes
3
replies
469
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
0
votes
3
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556
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Need help interpreting heatmaps from limma
limma
written 6 months ago by • 0
2
votes
1
reply
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
votes
4
replies
727
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
vote
2
replies
643
views
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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335
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
6 months ago tim.meese • 0
0
votes
2
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551
views
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
votes
2
replies
613
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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7.5k
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
votes
1
reply
530
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
votes
1
reply
1.5k
views
Unable to install/use limma
limma Bioconductor
updated 7 months ago by 68k • written 7 months ago by • 0
3
votes
3
replies
754
views
voom does not seem to properly correct for library size
limma
updated 7 months ago by 52k • written 7 months ago by ★ 4.8k
50 results • Page 1 of 1
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Comment: DeSeq Strategies for run to run Replication by Michael Love 43k
You shouldn't need to run `DESeq` on the test data, or manually compute normalization factors. ``` dds_test <- ... # create object dds_te…
Answer: Feature Counts - potential bug with outfile.jcounts by Wei Shi ★ 3.6k
We have made significant changes to how featureCounts annotates junctions detected in read mapping results. These updates are included in t…
Comment: How to perform batch correction on scRNA-seq with confounding plate effects? by 瑞宏 • 0
I would like to share my own understanding: in single-cell RNA sequencing (scRNA-seq), batch correction is solely intended to identify the …
Comment: DiffBind can't find a DAR by Mengjun • 0
Additionally, i checked my bigwig in igv, it shows that the ctrl_1 is more like ko_1, and ctrl_2's track is more like ko_2's track. Did an…
Comment: European Bioconductor Conference 2023 planning by ht • 0
Great news about the European Bioconductor Conference 2023 planning! As someone who enjoys statistical computing and bioinformatics, I'm ex…
Votes
Comment: Differential expression analysis using two TCGA datasets
C: Annotating HTA 2.0 genes
C: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
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