Showing : LIMMA • reset
1
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7
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619
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
3 days ago • updated 5 hours ago Adam Marstrand • 0
1
vote
2
replies
800
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
2 days ago Ai • 0
3
votes
2
replies
643
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
updated 10 days ago by ★ 4.5k • written 11 days ago by • 0
4
votes
3
replies
692
views
Analysis of 2*4 factorial design
limma
updated 7 days ago by 51k • written 14 days ago by • 0
2
votes
9
replies
1.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
updated 1 day ago by 51k • written 13 days ago by • 0
4
votes
6
replies
1.3k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 15 days ago by 51k • written 16 days ago by • 0
4
votes
6
replies
971
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
20 days ago • updated 11 days ago altintas.ali • 0
2
votes
2
replies
247
views
Automatically generate contrasts from a model matrix / formula
limma
updated 22 days ago by ★ 4.5k • written 23 days ago by ▴ 10
3
votes
3
replies
241
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
27 days ago • updated 24 days ago Guido Hooiveld ★ 4.1k
0
votes
3
replies
275
views
Need help interpreting heatmaps from limma
limma
written 26 days ago by • 0
2
votes
1
reply
1.3k
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 28 days ago by 67k • written 29 days ago by ▴ 10
5
votes
4
replies
391
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 4 weeks ago by ★ 4.5k • written 5 weeks ago by • 0
1
vote
2
replies
405
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 10
0
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0
replies
194
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
5 weeks ago tim.meese • 0
0
votes
2
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302
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 weeks ago by 51k • written 6 weeks ago by • 0
0
votes
2
replies
400
views
Question on performing ANOVA-like analysis using limma
limma
updated 6 weeks ago by 51k • written 6 weeks ago by • 0
17
votes
9
replies
6.9k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 weeks ago by 67k • written 8.4 years ago by ▴ 10
2
votes
1
reply
311
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 7 weeks ago by 67k • written 7 weeks ago by ▴ 10
0
votes
1
reply
371
views
Unable to install/use limma
limma Bioconductor
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
3
votes
3
replies
439
views
voom does not seem to properly correct for library size
limma
updated 10 weeks ago by 51k • written 10 weeks ago by ★ 4.5k
1
vote
5
replies
737
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 10 weeks ago by 51k • written 11 weeks ago by • 0
0
votes
3
replies
492
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 11 weeks ago by 51k • written 11 weeks ago by • 0
3
votes
4
replies
501
views
using limma trend workflow in CAMERA
CAMERA limma
12 weeks ago • updated 10 weeks ago Jay • 0
3
votes
3
replies
486
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 12 weeks ago by 51k • written 12 weeks ago by ▴ 10
1
vote
6
replies
638
views
limma and Syntactically Invalid Factor Values
limma
updated 3 months ago by 51k • written 3 months ago by ★ 1.5k
1
vote
1
reply
482
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
3 months ago Bioinformagician • 0
4
votes
3
replies
492
views
Limma comparing gene expression between base line and one treatment
limma
updated 3 months ago by 67k • written 3 months ago by • 0
0
votes
1
reply
399
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 3 months ago by ★ 4.5k • written 3 months ago by • 0
2
votes
5
replies
567
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 3 months ago by 67k • written 3 months ago by • 0
4
votes
14
replies
1.5k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 3 months ago by 51k • written 3 months ago by • 0
3
votes
4
replies
771
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
4 months ago jcollier • 0
4
votes
4
replies
1.1k
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
4 months ago sukeshinik5 ▴ 20
0
votes
1
reply
292
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 4 months ago by 67k • written 4 months ago by • 0
3
votes
3
replies
450
views
Warning message when running limma with covariates
limma
updated 4 months ago by 51k • written 4 months ago by ▴ 20
0
votes
8
replies
1.5k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
4 months ago • updated 3 months ago jiachengd • 0
5
votes
4
replies
622
views
Limma with covariates
limma
4 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 5 months ago by • 0
3
votes
2
replies
591
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
422
views
Subsetting RNAseq data | voomaByGroup()
limma
5 months ago Anna • 0
1
vote
2
replies
571
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
6 months ago Dylan.Sheerin • 0
2
votes
2
replies
647
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
6 months ago • updated 5 months ago user_bioinfo • 0
3
votes
10
replies
955
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 6 months ago by 67k • written 6 months ago by • 0
3
votes
2
replies
735
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 5 months ago by 51k • written 6 months ago by • 0
0
votes
1
reply
396
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 6 months ago by 51k • written 6 months ago by • 0
3
votes
4
replies
547
views
Help with error using camera() in limma
CAMERA limma
6 months ago Chris ▴ 20
0
votes
3
replies
502
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
0
votes
2
replies
424
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 6 months ago by • 0
0
votes
2
replies
548
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
6 months ago catv • 0
15
votes
17
replies
2.1k
views
Why p value inconsistent when using different number of pathway score?
limma
6 months ago Chris ▴ 20
5
votes
3
replies
783
views
Log-cpm values from limma
limma edgeR RNASeq
updated 6 months ago by 51k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Problem at champ.load by icecreamlover • 0
Hello! Were you able to figure this out? I am running into the same error!
Comment: ChAMP - obtaining beta values using EPICv2 annotation by icecreamlover • 0
Hello, Were you able to fix the error? I used the same document and I am running into the same error. I am curious if you have any feedba…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
Can this please be revisited and corrected ASAP? I'm encountering the same issue, using a slightly more modern version of R (4.1.0). It s…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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