Showing : Limma • reset
2
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
12 days ago • updated just now svlachavas ▴ 840
3
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5
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1.1k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 6 weeks ago by 68k • written 6 weeks ago by ▴ 10
0
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0
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160
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
7 weeks ago GJ • 0
0
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2
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429
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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 7 weeks ago by ▴ 840
2
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5
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389
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Differential variability modelling with vst() expression
limma DESeq2
written 7 weeks ago by • 0
6
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5
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646
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 7 weeks ago by 68k • written 8 weeks ago by • 0
0
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2
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516
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Cross-validation with multiple control subgroups in limma
limma multtest
10 weeks ago Ali Barry ▴ 40
1
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9
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914
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 10 weeks ago by ▴ 30
0
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2
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368
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
12 weeks ago • updated 11 weeks ago Tadeoye ▴ 20
0
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2
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539
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 weeks ago by 52k • written 12 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 12 weeks ago by 68k • written 12 weeks ago by ▴ 10
1
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2
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471
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contrast matrix design for a continuous variable
limma
3 months ago • updated 6 weeks ago dtzhu337 • 0
3
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3
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689
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Crossover design with limma
limma crossover
updated 11 weeks ago by 52k • written 3 months ago by ▴ 30
0
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9
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1.1k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 12 weeks ago by 68k • written 3 months ago by • 0
6
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10
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2.7k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 12 weeks ago by ★ 4.7k • written 3 months ago by ▴ 10
1
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3
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507
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 3 months ago by • 0
0
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2
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250
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
3 months ago giulia.gentile ▴ 10
4
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2
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660
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 3 months ago by 52k • written 3 months ago by ▴ 50
1
vote
2
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292
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Limma Interaction Effect with Covariates
limma DMRcate
3 months ago kitzhu • 0
2
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3
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977
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[How to construct a model.matrix ]
limma modelmatrix
updated 3 months ago by 52k • written 3 months ago by • 0
3
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4
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775
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
3 months ago dseauer • 0
1
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3
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531
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
3 months ago abadgerw • 0
0
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5
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777
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
3 months ago abadgerw • 0
1
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8
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1.4k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 3 months ago by • 0
1
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2
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1.0k
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
3 months ago Ai • 0
3
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3
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1.0k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 4 months ago by • 0
4
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3
replies
880
views
Analysis of 2*4 factorial design
limma
updated 4 months ago by 52k • written 4 months ago by • 0
2
votes
12
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1.9k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
4 months ago • updated 3 months ago john • 0
4
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6
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1.6k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 4 months ago by 52k • written 4 months ago by • 0
4
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6
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1.3k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
4 months ago altintas.ali • 0
2
votes
2
replies
471
views
Automatically generate contrasts from a model matrix / formula
limma
updated 4 months ago by ★ 4.7k • written 4 months ago by ▴ 10
3
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3
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405
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
4 months ago Guido Hooiveld ★ 4.1k
0
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3
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480
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Need help interpreting heatmaps from limma
limma
written 4 months ago by • 0
2
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1
reply
1.6k
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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 4 months ago by 68k • written 4 months ago by ▴ 10
5
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4
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608
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 months ago by ★ 4.7k • written 5 months ago by • 0
1
vote
2
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577
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
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0
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292
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
5 months ago tim.meese • 0
0
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2
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481
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
0
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2
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552
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Question on performing ANOVA-like analysis using limma
limma
updated 5 months ago by 52k • written 5 months ago by • 0
17
votes
9
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7.4k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 5 months ago by 68k • written 8.8 years ago by ▴ 10
2
votes
1
reply
448
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 5 months ago by 68k • written 5 months ago by ▴ 10
0
votes
1
reply
1.1k
views
Unable to install/use limma
limma Bioconductor
updated 6 months ago by 68k • written 6 months ago by • 0
3
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3
replies
651
views
voom does not seem to properly correct for library size
limma
updated 6 months ago by 52k • written 6 months ago by ★ 4.7k
1
vote
5
replies
945
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 6 months ago by 52k • written 6 months ago by • 0
0
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3
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644
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 6 months ago by 52k • written 6 months ago by • 0
3
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4
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761
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using limma trend workflow in CAMERA
CAMERA limma
6 months ago Jay • 0
3
votes
3
replies
685
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One-sided tests with CAMERA-PR
CAMERA limma
updated 6 months ago by 52k • written 6 months ago by ▴ 10
1
vote
6
replies
837
views
limma and Syntactically Invalid Factor Values
limma
updated 7 months ago by 52k • written 7 months ago by ★ 1.6k
1
vote
1
reply
731
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
7 months ago Bioinformagician • 0
4
votes
3
replies
713
views
Limma comparing gene expression between base line and one treatment
limma
updated 7 months ago by 68k • written 7 months ago by • 0
50 results • Page 1 of 1
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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
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