Showing : LIMMA • reset
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 11 months ago by • 0
0
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2
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400
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
11 months ago giulia.gentile ▴ 10
4
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2
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1.2k
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 11 months ago by 53k • written 11 months ago by ▴ 60
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2
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489
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Limma Interaction Effect with Covariates
limma DMRcate
11 months ago kitzhu • 0
2
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3
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1.3k
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[How to construct a model.matrix ]
limma modelmatrix
updated 11 months ago by 53k • written 11 months ago by • 0
3
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4
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1.1k
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
11 months ago dseauer • 0
1
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3
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814
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
11 months ago • updated 10 months ago abadgerw • 0
0
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5
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1.1k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
11 months ago • updated 10 months ago abadgerw • 0
1
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8
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2.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 11 months ago by • 0
1
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2
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1.4k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
11 months ago Ai • 0
3
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3
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1.5k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 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 11 months ago by 53k • written 12 months ago by • 0
2
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12
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2.6k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
12 months ago • updated 11 months ago john • 0
4
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6
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1.9k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 12 months ago by 53k • written 12 months ago by • 0
4
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6
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1.7k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
12 months ago • updated 11 months ago altintas.ali • 0
2
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2
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828
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Automatically generate contrasts from a model matrix / formula
limma
updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
3
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3
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708
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
12 months ago Guido Hooiveld ★ 4.1k
0
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3
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711
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Need help interpreting heatmaps from limma
limma
written 12 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 12 months ago by 68k • written 12 months ago by ▴ 10
5
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4
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960
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
1
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2
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843
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 months ago by 43k • written 13 months ago by ▴ 10
0
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0
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453
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
12 months ago tim.meese • 0
0
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2
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758
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 12 months ago by 53k • written 13 months ago by • 0
0
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2
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690
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Question on performing ANOVA-like analysis using limma
limma
updated 13 months ago by 53k • written 13 months ago by • 0
17
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9
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8.2k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 13 months ago by 68k • written 9.4 years ago by ▴ 10
2
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1
reply
684
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 13 months ago by 68k • written 13 months ago by ▴ 20
0
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1
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2.0k
views
Unable to install/use limma
limma Bioconductor
updated 13 months ago by 68k • written 13 months ago by • 0
3
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3
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920
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voom does not seem to properly correct for library size
limma
updated 13 months ago by 53k • written 14 months ago by ★ 5.0k
1
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5
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1.4k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 14 months ago by 53k • written 14 months ago by • 0
0
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3
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889
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 14 months ago by 53k • written 14 months ago by • 0
3
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4
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1.2k
views
using limma trend workflow in CAMERA
CAMERA limma
14 months ago • updated 13 months ago Jiahao Tian • 0
3
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3
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948
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One-sided tests with CAMERA-PR
CAMERA limma
updated 14 months ago by 53k • written 14 months ago by ▴ 10
1
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6
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1.2k
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limma and Syntactically Invalid Factor Values
limma
updated 15 months ago by 53k • written 15 months ago by ★ 1.6k
1
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1
reply
992
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DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
15 months ago Bioinformagician • 0
5
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3
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1.0k
views
Limma comparing gene expression between base line and one treatment
limma
updated 15 months ago by 68k • written 15 months ago by • 0
0
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1
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1.1k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
2
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5
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1.1k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
4
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14
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2.5k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 14 months ago by 53k • written 15 months ago by • 0
3
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4
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1.2k
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Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
15 months ago jcollier • 0
4
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4
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1.7k
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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
16 months ago sukeshinik5 ▴ 20
0
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1
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539
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 16 months ago by 68k • written 16 months ago by • 0
4
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4
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1.0k
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Warning message when running limma with covariates
limma
16 months ago • updated 9 months ago Chris ▴ 20
0
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8
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2.1k
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limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
16 months ago • updated 15 months ago jiachengd • 0
5
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5
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1.6k
views
Limma with covariates
limma
written 16 months ago by ▴ 20
3
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13
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1.9k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 16 months ago by • 0 • written 16 months ago by • 0
3
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2
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1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
17 months ago mohammedtoufiq91 ▴ 10
1
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2
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766
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Subsetting RNAseq data | voomaByGroup()
limma
17 months ago Anna • 0
1
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2
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1.0k
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
17 months ago Dylan.Sheerin • 0
2
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2
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1.2k
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
17 months ago user_bioinfo • 0
3
votes
10
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1.8k
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 17 months ago by 68k • written 17 months ago by • 0
4,225 results • Page 2 of 85
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by dzv20413 • 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments by Erik Wright ▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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