Showing : Limma • reset
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
21 hours ago GJ • 0
0
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2
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325
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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 days ago by ▴ 840
2
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4
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210
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Differential variability modelling with vst() expression
limma DESeq2
updated 4 days ago by 43k • written 4 days ago by • 0
6
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5
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509
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 6 days ago by 67k • written 12 days ago by • 0
0
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2
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430
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Cross-validation with multiple control subgroups in limma
limma multtest
24 days ago • updated 23 days ago Ali Barry ▴ 40
1
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9
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763
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 27 days ago by ▴ 30
0
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2
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295
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
5 weeks ago • updated 4 weeks ago Tadeoye ▴ 20
0
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2
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479
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 5 weeks ago by 52k • written 5 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 5 weeks ago by 67k • written 5 weeks ago by ▴ 10
1
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2
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337
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contrast matrix design for a continuous variable
limma
6 weeks ago dtzhu337 • 0
3
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3
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620
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Crossover design with limma
limma crossover
updated 28 days ago by 52k • written 6 weeks ago by ▴ 30
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9
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896
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 5 weeks ago by 67k • written 6 weeks ago by • 0
6
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10
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2.5k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 5 weeks ago by ★ 4.6k • written 6 weeks ago by ▴ 10
1
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3
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438
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 7 weeks ago by • 0
0
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2
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203
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
8 weeks ago • updated 7 weeks ago giulia.gentile ▴ 10
4
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2
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560
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 8 weeks ago by 52k • written 8 weeks ago by ▴ 50
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2
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197
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Limma Interaction Effect with Covariates
limma DMRcate
8 weeks ago kitzhu • 0
2
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3
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907
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[How to construct a model.matrix ]
limma modelmatrix
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
3
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4
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662
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
8 weeks ago dseauer • 0
1
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3
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459
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
9 weeks ago • updated 6 weeks ago abadgerw • 0
0
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5
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671
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
9 weeks ago • updated 6 weeks ago abadgerw • 0
1
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8
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1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 10 weeks ago by • 0
1
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2
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958
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
10 weeks ago • updated 9 weeks ago Ai • 0
3
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3
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937
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 weeks ago by • 0
4
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3
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819
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Analysis of 2*4 factorial design
limma
updated 10 weeks ago by 52k • written 11 weeks ago by • 0
2
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12
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1.7k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
11 weeks ago • updated 7 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 11 weeks ago by 52k • written 11 weeks 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
12 weeks ago • updated 11 weeks ago altintas.ali • 0
2
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2
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365
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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340
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
3 months ago Guido Hooiveld ★ 4.1k
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3
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390
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Need help interpreting heatmaps from limma
limma
written 3 months ago by • 0
2
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1
reply
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
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4
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518
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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502
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 3 months ago by 43k • written 3 months ago by ▴ 10
0
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0
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249
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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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411
views
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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489
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Question on performing ANOVA-like analysis using limma
limma
updated 3 months ago by 52k • written 3 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 3 months ago by 67k • written 8.6 years ago by ▴ 10
2
votes
1
reply
381
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
725
views
Unable to install/use limma
limma Bioconductor
updated 4 months ago by 67k • written 4 months ago by • 0
3
votes
3
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564
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
vote
5
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858
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 4 months ago by 52k • written 4 months ago by • 0
0
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3
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588
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 4 months ago by 52k • written 4 months ago by • 0
3
votes
4
replies
662
views
using limma trend workflow in CAMERA
CAMERA limma
5 months ago • updated 4 months ago Jay • 0
3
votes
3
replies
602
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 5 months ago by 52k • written 5 months ago by ▴ 10
1
vote
6
replies
737
views
limma and Syntactically Invalid Factor Values
limma
updated 5 months ago by 52k • written 5 months ago by ★ 1.5k
1
vote
1
reply
624
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
5 months ago Bioinformagician • 0
4
votes
3
replies
614
views
Limma comparing gene expression between base line and one treatment
limma
updated 5 months ago by 67k • written 6 months ago by • 0
0
votes
1
reply
581
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
2
votes
5
replies
666
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 5 months ago by 67k • written 6 months ago by • 0
50 results • Page 1 of 1
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
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