Showing : LIMMA • reset
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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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3.5k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 12 months ago by ★ 5.0k • written 13 months ago by ▴ 10
1
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3
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828
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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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429
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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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529
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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
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[How to construct a model.matrix ]
limma modelmatrix
updated 13 months ago by 53k • written 13 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
13 months ago dseauer • 0
1
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3
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918
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
13 months ago abadgerw • 0
0
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5
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1.2k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
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
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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
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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
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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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1.9k
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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947
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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
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795
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
14 months ago Guido Hooiveld ★ 4.1k
0
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3
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778
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Need help interpreting heatmaps from limma
limma
written 14 months ago by • 0
2
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1
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2.0k
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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 14 months ago by 68k • written 14 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 14 months ago by ★ 5.0k • written 15 months ago by • 0
1
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2
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925
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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492
views
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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830
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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734
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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8.4k
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
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1
reply
779
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 15 months ago by 68k • written 15 months ago by ▴ 20
0
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1
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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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981
views
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
16 months ago Jiahao Tian • 0
3
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3
replies
1.0k
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 16 months ago by 53k • written 16 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
views
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 17 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 • updated 17 months ago jcollier • 0
4
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4
replies
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
587
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
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
18 months ago • updated 17 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
votes
13
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2.1k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 18 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
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Votes
Error in SummarizedExperiment(assays = SimpleList(counts = countData)
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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