Showing : Limma • reset
0
votes
2
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66
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How to subset voomLmFit (MArrayLM) object?
limma edgeR
updated 1 hour ago by 51k • written 1 day ago by ★ 4.1k
0
votes
1
reply
64
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Need help interpreting heatmaps from limma
limma
updated 23 hours ago by 67k • written 1 day ago by • 0
2
votes
1
reply
490
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 days ago by 67k • written 3 days ago by ▴ 10
5
votes
4
replies
300
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 days ago by ★ 4.5k • written 9 days ago by • 0
1
vote
2
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346
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 days ago by 42k • written 19 days ago by ▴ 10
0
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0
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165
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
15 days ago • updated 14 days ago tim.meese • 0
0
votes
2
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251
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 13 days ago by 51k • written 18 days ago by • 0
0
votes
2
replies
360
views
Question on performing ANOVA-like analysis using limma
limma
updated 21 days ago by 51k • written 22 days ago by • 0
17
votes
9
replies
6.8k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 26 days ago by 67k • written 8.4 years ago by ▴ 10
2
votes
1
reply
272
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 29 days ago by 67k • written 29 days ago by ▴ 10
0
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1
reply
276
views
Unable to install/use limma
limma Bioconductor
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
3
votes
3
replies
371
views
voom does not seem to properly correct for library size
limma
updated 6 weeks ago by 51k • written 6 weeks ago by ★ 4.5k
1
vote
5
replies
693
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 6 weeks ago by 51k • written 7 weeks ago by • 0
0
votes
3
replies
458
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 7 weeks ago by 51k • written 7 weeks ago by • 0
3
votes
4
replies
462
views
using limma trend workflow in CAMERA
CAMERA limma
8 weeks ago • updated 6 weeks ago Jay • 0
3
votes
3
replies
449
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 8 weeks ago by 51k • written 8 weeks ago by ▴ 10
1
vote
6
replies
574
views
limma and Syntactically Invalid Factor Values
limma
updated 11 weeks ago by 51k • written 11 weeks ago by ★ 1.5k
1
vote
1
reply
423
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
12 weeks ago • updated 11 weeks ago Bioinformagician • 0
4
votes
3
replies
454
views
Limma comparing gene expression between base line and one treatment
limma
updated 12 weeks ago by 67k • written 12 weeks ago by • 0
0
votes
1
reply
337
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 12 weeks ago by ★ 4.5k • written 12 weeks ago by • 0
2
votes
5
replies
505
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 11 weeks ago by 67k • written 12 weeks ago by • 0
4
votes
14
replies
1.4k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 10 weeks ago by 51k • written 12 weeks ago by • 0
3
votes
4
replies
743
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
3 months ago jcollier • 0
4
votes
4
replies
1.0k
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
3 months ago sukeshinik5 • 0
0
votes
1
reply
267
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 3 months ago by 67k • written 3 months ago by • 0
3
votes
3
replies
411
views
Warning message when running limma with covariates
limma
updated 3 months ago by 51k • written 3 months ago by ▴ 20
0
votes
8
replies
1.4k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
3 months ago jiachengd • 0
5
votes
4
replies
559
views
Limma with covariates
limma
3 months ago Chris ▴ 20
3
votes
13
replies
1.2k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 4 months ago by • 0 • written 4 months ago by • 0
3
votes
2
replies
545
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
4 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
394
views
Subsetting RNAseq data | voomaByGroup()
limma
4 months ago Anna • 0
1
vote
2
replies
542
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
5 months ago Dylan.Sheerin • 0
2
votes
2
replies
590
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
5 months ago user_bioinfo • 0
3
votes
10
replies
907
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 5 months ago by 67k • written 5 months ago by • 0
3
votes
2
replies
709
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 4 months ago by 51k • written 5 months ago by • 0
0
votes
1
reply
374
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 5 months ago by 51k • written 5 months ago by • 0
3
votes
4
replies
512
views
Help with error using camera() in limma
CAMERA limma
5 months ago Chris ▴ 20
0
votes
3
replies
475
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
2
replies
396
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 5 months ago by • 0
0
votes
2
replies
503
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 months ago catv • 0
15
votes
17
replies
2.0k
views
Why p value inconsistent when using different number of pathway score?
limma
5 months ago Chris ▴ 20
5
votes
3
replies
709
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 months ago by 51k • written 5 months ago by • 0
0
votes
7
replies
997
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
5 months ago hortense96 • 0
1
vote
3
replies
582
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 6 months ago by 51k • written 6 months ago by • 0
5
votes
9
replies
1.4k
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
6 months ago • updated 5 months ago Chris ▴ 20
2
votes
6
replies
1.5k
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
6 months ago Chris ▴ 20
0
votes
1
reply
323
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
4
replies
559
views
Help with design.matrix
limma
6 months ago andrea.rodriguez-martinez13 • 0
1
vote
4
replies
668
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 6 months ago by 51k • written 6 months ago by • 0
0
votes
2
replies
427
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 months ago Gimena • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to subset voomLmFit (MArrayLM) object? by Gordon Smyth 51k
Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…
Answer: Need help interpreting heatmaps from limma by James W. MacDonald 67k
Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …
Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file by James W. MacDonald 67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
Votes
Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
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