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 6 days ago by 67k • written 6 days ago by ▴ 10
0
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0
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74
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 days ago GJ • 0
0
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2
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356
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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 12 days ago by ▴ 840
2
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5
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291
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Differential variability modelling with vst() expression
limma DESeq2
written 13 days ago by • 0
6
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5
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532
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 15 days ago by 67k • written 21 days ago by • 0
0
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2
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460
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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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809
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 5 weeks ago by ▴ 30
0
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2
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310
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
6 weeks ago Tadeoye ▴ 20
0
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2
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487
views
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
votes
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 7 weeks ago by ▴ 10
1
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2
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411
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contrast matrix design for a continuous variable
limma
7 weeks ago • updated 2 days ago dtzhu337 • 0
3
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3
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630
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Crossover design with limma
limma crossover
updated 5 weeks ago by 52k • written 7 weeks ago by ▴ 30
0
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9
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915
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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 8 weeks ago by ▴ 10
1
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3
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445
views
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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209
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
9 weeks ago giulia.gentile ▴ 10
4
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2
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579
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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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235
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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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912
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[How to construct a model.matrix ]
limma modelmatrix
updated 9 weeks ago by 52k • written 10 weeks ago by • 0
3
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4
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671
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
10 weeks ago dseauer • 0
1
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3
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475
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 8 weeks ago abadgerw • 0
0
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5
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686
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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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969
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
11 weeks ago Ai • 0
3
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3
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947
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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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831
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Analysis of 2*4 factorial design
limma
updated 12 weeks ago by 52k • written 3 months 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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386
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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348
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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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401
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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
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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 3 months ago by 67k • written 3 months ago by ▴ 10
5
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4
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524
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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513
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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415
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 3 months ago by 52k • written 4 months ago by • 0
0
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2
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497
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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
390
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
votes
1
reply
779
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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576
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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870
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 5 months ago by 52k • written 5 months ago by • 0
0
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3
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593
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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673
views
using limma trend workflow in CAMERA
CAMERA limma
5 months ago • updated 4 months ago Jay • 0
3
votes
3
replies
614
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 5 months ago by 52k • written 5 months ago by ▴ 10
1
vote
6
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752
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
642
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
replies
626
views
Limma comparing gene expression between base line and one treatment
limma
updated 6 months ago by 67k • written 6 months ago by • 0
0
votes
1
reply
607
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
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Votes
Answer: DESeq2- merging technical vs biological replicates
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
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