Showing : Limma • reset
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 15 days ago by 67k • written 15 days ago by ▴ 10
0
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0
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127
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
19 days ago GJ • 0
0
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2
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372
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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 22 days ago by ▴ 840
2
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5
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321
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Differential variability modelling with vst() expression
limma DESeq2
written 22 days ago by • 0
6
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5
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566
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 25 days ago by 67k • written 4 weeks ago by • 0
0
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2
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485
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Cross-validation with multiple control subgroups in limma
limma multtest
6 weeks ago • updated 5 weeks ago Ali Barry ▴ 40
1
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9
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846
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 6 weeks ago by ▴ 30
0
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2
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328
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
7 weeks ago Tadeoye ▴ 20
0
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2
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497
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 8 weeks ago by 52k • written 8 weeks ago by ▴ 10
2
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3
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1.3k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 8 weeks ago by 67k • written 8 weeks ago by ▴ 10
1
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2
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434
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contrast matrix design for a continuous variable
limma
8 weeks ago • updated 11 days ago dtzhu337 • 0
3
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3
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646
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Crossover design with limma
limma crossover
updated 6 weeks ago by 52k • written 9 weeks ago by ▴ 30
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9
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962
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 8 weeks ago by 67k • written 9 weeks ago by • 0
6
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10
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2.6k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 7 weeks ago by ★ 4.6k • written 9 weeks ago by ▴ 10
1
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3
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459
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 10 weeks ago by • 0
0
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2
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220
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
10 weeks ago giulia.gentile ▴ 10
4
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2
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603
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 50
1
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2
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250
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Limma Interaction Effect with Covariates
limma DMRcate
10 weeks ago kitzhu • 0
2
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3
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928
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[How to construct a model.matrix ]
limma modelmatrix
updated 10 weeks ago by 52k • written 11 weeks ago by • 0
3
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4
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690
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
11 weeks ago dseauer • 0
1
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3
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489
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
12 weeks ago • updated 9 weeks ago abadgerw • 0
0
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5
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716
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
12 weeks ago • updated 8 weeks ago abadgerw • 0
1
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8
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1.3k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 12 weeks ago by • 0
1
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2
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984
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
12 weeks ago Ai • 0
3
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3
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966
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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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847
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Analysis of 2*4 factorial design
limma
updated 3 months ago by 52k • written 3 months ago by • 0
2
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12
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1.8k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
3 months ago • updated 10 weeks ago john • 0
4
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6
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1.5k
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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
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
3 months ago altintas.ali • 0
2
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2
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413
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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364
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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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420
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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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540
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 3 months ago by ★ 4.6k • written 4 months ago by • 0
1
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2
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533
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
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0
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264
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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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444
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
0
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2
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515
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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 8.7 years ago by ▴ 10
2
votes
1
reply
405
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
845
views
Unable to install/use limma
limma Bioconductor
updated 5 months ago by 67k • written 5 months ago by • 0
3
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3
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589
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voom does not seem to properly correct for library size
limma
updated 5 months ago by 52k • written 5 months ago by ★ 4.6k
1
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5
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884
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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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603
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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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691
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using limma trend workflow in CAMERA
CAMERA limma
5 months ago Jay • 0
3
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3
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632
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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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767
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limma and Syntactically Invalid Factor Values
limma
updated 6 months ago by 52k • written 6 months ago by ★ 1.5k
1
vote
1
reply
659
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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640
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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
640
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
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Replies
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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