Showing : Limma • reset
1
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753
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contrast matrix design for a continuous variable
limma
13 months ago • updated 11 months ago dtzhu337 • 0
3
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3
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1.1k
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Crossover design with limma
limma crossover
updated 12 months ago by 53k • written 13 months ago by ▴ 30
0
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9
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1.8k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 13 months ago by 68k • written 13 months ago by • 0
6
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10
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3.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
1
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3
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840
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 13 months ago by • 0
0
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2
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430
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
13 months ago giulia.gentile ▴ 10
4
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2
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1.4k
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 13 months ago by 53k • written 13 months ago by ▴ 60
1
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2
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539
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Limma Interaction Effect with Covariates
limma DMRcate
13 months ago kitzhu • 0
2
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3
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1.4k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 13 months ago by 53k • written 14 months ago by • 0
3
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4
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1.2k
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
14 months ago • updated 13 months ago dseauer • 0
1
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3
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931
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
0
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5
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1.2k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
1
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8
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2.6k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 14 months ago by • 0
1
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2
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1.5k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
14 months ago Ai • 0
3
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3
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1.6k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 14 months ago by • 0
4
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3
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1.2k
views
Analysis of 2*4 factorial design
limma
updated 14 months ago by 53k • written 14 months ago by • 0
2
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12
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2.8k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
14 months ago • updated 13 months ago john • 0
4
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6
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2.0k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 14 months ago by 53k • written 14 months ago by • 0
4
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6
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1.9k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
14 months ago altintas.ali • 0
2
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2
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972
views
Automatically generate contrasts from a model matrix / formula
limma
updated 14 months ago by ★ 5.0k • written 14 months ago by ▴ 10
3
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3
replies
803
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
15 months ago Guido Hooiveld ★ 4.1k
0
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3
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788
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Need help interpreting heatmaps from limma
limma
written 15 months ago by • 0
2
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1
reply
2.0k
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 15 months ago by 68k • written 15 months ago by ▴ 10
5
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4
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1.1k
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
1
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2
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936
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 15 months ago by 43k • written 15 months ago by ▴ 10
0
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0
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499
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
15 months ago tim.meese • 0
0
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2
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838
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 15 months ago by 53k • written 15 months ago by • 0
0
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2
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739
views
Question on performing ANOVA-like analysis using limma
limma
updated 15 months ago by 53k • written 15 months ago by • 0
17
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9
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8.5k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 15 months ago by 68k • written 9.6 years ago by ▴ 10
2
votes
1
reply
787
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 16 months ago by 68k • written 16 months ago by ▴ 20
0
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1
reply
2.3k
views
Unable to install/use limma
limma Bioconductor
updated 16 months ago by 68k • written 16 months ago by • 0
3
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3
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987
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voom does not seem to properly correct for library size
limma
updated 16 months ago by 53k • written 16 months ago by ★ 5.0k
1
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5
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1.5k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 16 months ago by 53k • written 16 months ago by • 0
0
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3
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1.0k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 16 months ago by 53k • written 16 months ago by • 0
3
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4
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1.4k
views
using limma trend workflow in CAMERA
CAMERA limma
17 months ago • updated 16 months ago Jiahao Tian • 0
3
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3
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1.0k
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 17 months ago by 53k • written 17 months ago by ▴ 10
1
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6
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1.3k
views
limma and Syntactically Invalid Factor Values
limma
updated 17 months ago by 53k • written 17 months ago by ★ 1.6k
1
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1
reply
1.1k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
17 months ago Bioinformagician • 0
5
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3
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1.1k
views
Limma comparing gene expression between base line and one treatment
limma
updated 17 months ago by 68k • written 17 months ago by • 0
0
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1
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1.2k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
2
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5
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1.2k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
4
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14
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2.7k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 17 months ago by 53k • written 18 months ago by • 0
3
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4
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1.3k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
18 months ago jcollier • 0
4
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4
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1.8k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
18 months ago sukeshinik5 ▴ 20
0
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1
reply
599
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 18 months ago by 68k • written 18 months ago by • 0
4
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4
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1.2k
views
Warning message when running limma with covariates
limma
18 months ago • updated 12 months ago Chris ▴ 20
0
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8
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2.3k
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limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
18 months ago jiachengd • 0
5
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5
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1.8k
views
Limma with covariates
limma
written 18 months ago by ▴ 20
3
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13
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2.1k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 19 months ago by • 0 • written 19 months ago by • 0
3
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2
replies
1.3k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
19 months ago mohammedtoufiq91 ▴ 10
4,228 results • Page 2 of 85
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub? by jwp48 • 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond by Ludwig Geistlinger ▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
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