Showing : Limma • reset
0
votes
2
replies
247
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 hours ago by ★ 4.8k • written 22 hours ago by • 0
1
vote
3
replies
225
views
Explanation for ROAST results
CAMERA limma
updated 11 hours ago by 52k • written 1 day ago by • 0
5
votes
3
replies
742
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 6 days ago by 52k • written 7 days ago by ▴ 10
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
15 days ago • updated 9 days ago Elizabeth • 0
1
vote
8
replies
1.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
5
votes
5
replies
1.1k
views
Limma with covariates
limma
written 9 months ago by ▴ 20
1
vote
2
replies
760
views
Differential expression of proteins using somascan data
somascan limma
written 19 days ago by • 0
2
votes
4
replies
895
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
4 weeks ago • updated 22 days ago svlachavas ▴ 840
8
votes
6
replies
1.9k
views
Unbalanced experiment with multiple samples from each patient.
limma
updated 26 days ago by • 0 • written 7.3 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP limma Bioconductor ChAMPdata
updated 6 weeks ago by • 0 • written 3.6 years ago by • 0
1
vote
2
replies
497
views
contrast matrix design for a continuous variable
limma
3 months ago • updated 9 weeks ago dtzhu337 • 0
3
votes
5
replies
1.2k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by ▴ 10
2
votes
5
replies
444
views
Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
0
votes
0
replies
180
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
10 weeks ago GJ • 0
0
votes
2
replies
454
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 10 weeks ago by ▴ 840
6
votes
5
replies
687
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
4
votes
4
replies
782
views
Warning message when running limma with covariates
limma
9 months ago • updated 12 weeks ago Chris ▴ 20
1
vote
9
replies
977
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
0
votes
2
replies
545
views
Cross-validation with multiple control subgroups in limma
limma multtest
3 months ago Ali Barry ▴ 40
3
votes
3
replies
735
views
Crossover design with limma
limma crossover
updated 3 months ago by 52k • written 3 months ago by ▴ 30
0
votes
2
replies
401
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
3 months ago Tadeoye ▴ 20
6
votes
10
replies
2.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
0
votes
2
replies
575
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
2
votes
3
replies
1.4k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
votes
9
replies
1.1k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 3 months ago by 68k • written 3 months ago by • 0
1
vote
3
replies
531
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 4 months ago by • 0
0
votes
5
replies
815
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
1
vote
3
replies
557
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
2
votes
12
replies
2.1k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
5 months ago • updated 4 months ago john • 0
0
votes
2
replies
273
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
4 months ago giulia.gentile ▴ 10
4
votes
2
replies
698
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 4 months ago by 52k • written 4 months ago by ▴ 50
1
vote
2
replies
314
views
Limma Interaction Effect with Covariates
limma DMRcate
4 months ago kitzhu • 0
2
votes
3
replies
1.0k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 4 months ago by 52k • written 4 months ago by • 0
8
votes
3
replies
4.5k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 8.6 years ago by ▴ 10
3
votes
4
replies
822
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
4 months ago dseauer • 0
3
votes
3
replies
1.1k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 months ago by • 0
0
votes
1
reply
699
views
Issue with weights in voomLmFit()
limma
updated 4 months ago by 52k • written 17 months ago by ▴ 170
1
vote
2
replies
1.1k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
4 months ago Ai • 0
4
votes
3
replies
921
views
Analysis of 2*4 factorial design
limma
updated 4 months ago by 52k • written 5 months ago by • 0
4
votes
6
replies
1.4k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago altintas.ali • 0
3
votes
2
replies
2.0k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 5 months ago by 52k • written 3.3 years ago by • 0
11
votes
3
replies
2.5k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
written 16 months ago by • 0
4
votes
6
replies
1.7k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 5 months ago by 52k • written 5 months ago by • 0
0
votes
3
replies
525
views
Need help interpreting heatmaps from limma
limma
written 5 months ago by • 0
2
votes
2
replies
521
views
Automatically generate contrasts from a model matrix / formula
limma
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
34
votes
11
replies
42k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.3 years ago by ▴ 260
3
votes
3
replies
439
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
2
votes
1
reply
1.7k
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 5 months ago by 68k • written 5 months ago by ▴ 10
5
votes
4
replies
666
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
0
votes
2
replies
513
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
What is the cheapest day to fly on American Airlines? {Ask_Expert}
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to mdeea123 ▴ 10
Popular Question to GA ▴ 10
Popular Question to Elizabeth • 0
Popular Question to Kent • 0
Locations • All
United States, 7 minutes ago
United States, 11 minutes ago
United States, 24 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 679 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6