Showing : limma • reset
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
3 days ago • updated 8 hours ago svlachavas ▴ 840
3
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5
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1.1k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 5 weeks ago by 68k • written 5 weeks ago by ▴ 10
0
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0
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153
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
5 weeks ago GJ • 0
0
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2
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418
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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 6 weeks ago by ▴ 840
2
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5
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377
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Differential variability modelling with vst() expression
limma DESeq2
written 6 weeks ago by • 0
6
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5
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625
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 6 weeks ago by 68k • written 7 weeks ago by • 0
0
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2
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507
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Cross-validation with multiple control subgroups in limma
limma multtest
9 weeks ago Ali Barry ▴ 40
1
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9
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894
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 weeks ago by ▴ 30
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2
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356
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
10 weeks ago Tadeoye ▴ 20
0
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2
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522
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 11 weeks ago by 52k • written 11 weeks ago by ▴ 10
2
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3
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1.3k
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How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 11 weeks ago by 68k • written 11 weeks ago by ▴ 10
1
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2
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458
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contrast matrix design for a continuous variable
limma
11 weeks ago • updated 4 weeks ago dtzhu337 • 0
3
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3
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676
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Crossover design with limma
limma crossover
updated 9 weeks ago by 52k • written 12 weeks ago by ▴ 30
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9
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1.0k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
6
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10
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2.7k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 10 weeks ago by ★ 4.7k • written 12 weeks ago by ▴ 10
1
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3
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491
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 3 months ago by • 0
0
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2
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241
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
3 months ago giulia.gentile ▴ 10
4
votes
2
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639
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 3 months ago by 52k • written 3 months ago by ▴ 50
1
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2
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283
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Limma Interaction Effect with Covariates
limma DMRcate
3 months ago kitzhu • 0
2
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3
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962
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[How to construct a model.matrix ]
limma modelmatrix
updated 3 months ago by 52k • written 3 months ago by • 0
3
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4
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752
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
3 months ago dseauer • 0
1
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3
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515
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
3 months ago • updated 12 weeks ago abadgerw • 0
0
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5
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751
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
3 months ago • updated 11 weeks ago abadgerw • 0
1
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8
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1.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
1
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2
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1.0k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
3 months ago Ai • 0
3
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3
replies
1.0k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 3 months ago by • 0
4
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3
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872
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Analysis of 2*4 factorial design
limma
updated 3 months ago by 52k • written 4 months ago by • 0
2
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12
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1.9k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
4 months ago • updated 3 months ago john • 0
4
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6
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1.6k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 4 months ago by 52k • written 4 months ago by • 0
4
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6
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1.3k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 months ago • updated 3 months ago altintas.ali • 0
2
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2
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447
views
Automatically generate contrasts from a model matrix / formula
limma
updated 4 months ago by ★ 4.7k • written 4 months ago by ▴ 10
3
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3
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390
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
4 months ago Guido Hooiveld ★ 4.1k
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3
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462
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Need help interpreting heatmaps from limma
limma
written 4 months ago by • 0
2
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1
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1.6k
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 4 months ago by 68k • written 4 months ago by ▴ 10
5
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4
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576
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
1
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2
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561
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 5 months ago by ▴ 10
0
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0
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285
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
4 months ago tim.meese • 0
0
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2
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465
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 4 months ago by 52k • written 5 months ago by • 0
0
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2
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538
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Question on performing ANOVA-like analysis using limma
limma
updated 5 months ago by 52k • written 5 months ago by • 0
17
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9
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7.3k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 5 months ago by 68k • written 8.7 years ago by ▴ 10
2
votes
1
reply
437
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 5 months ago by 68k • written 5 months ago by ▴ 10
0
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1
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1.0k
views
Unable to install/use limma
limma Bioconductor
updated 5 months ago by 68k • written 5 months ago by • 0
3
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3
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630
views
voom does not seem to properly correct for library size
limma
updated 6 months ago by 52k • written 6 months ago by ★ 4.7k
1
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5
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929
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 6 months ago by 52k • written 6 months ago by • 0
0
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3
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629
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 6 months ago by 52k • written 6 months ago by • 0
3
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4
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733
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using limma trend workflow in CAMERA
CAMERA limma
6 months ago Jay • 0
3
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3
replies
668
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 6 months ago by 52k • written 6 months ago by ▴ 10
1
vote
6
replies
820
views
limma and Syntactically Invalid Factor Values
limma
updated 7 months ago by 52k • written 7 months ago by ★ 1.6k
1
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1
reply
707
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
7 months ago Bioinformagician • 0
4
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3
replies
688
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Limma comparing gene expression between base line and one treatment
limma
updated 7 months ago by 68k • written 7 months ago by • 0
50 results • Page 1 of 1
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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thanks a million for your reply (just saw it, did not get any notification through email) !! Regarding the log2 transformation…
Answer: cameraPR() non directional test by Gordon Smyth 52k
Yes, you can still do non-directional tests using cameraPR(), but it's not quite as easy as it was using the original camera() function as …
Answer: WGCNA with paired samples by Ivo • 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Votes
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: Plot title for PCA in DESeq2
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