Showing : limma • reset
0
votes
1
reply
71
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 2 hours ago by 52k • written 7 hours ago by • 0
1
vote
3
replies
145
views
Explannation for ROAST results
CAMERA limma
12 hours ago Jay • 0
5
votes
3
replies
740
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
0
votes
0
replies
40
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
11 days ago Geoff • 0
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
14 days ago • updated 8 days ago Elizabeth • 0
1
vote
2
replies
759
views
Differential expression of proteins using somascan data
somascan limma
written 18 days ago by • 0
2
votes
4
replies
893
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
4 weeks ago • updated 21 days ago svlachavas ▴ 840
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
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
452
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
2
votes
5
replies
444
views
Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
6
votes
5
replies
686
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
2
replies
545
views
Cross-validation with multiple control subgroups in limma
limma multtest
3 months ago Ali Barry ▴ 40
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
401
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
3 months ago Tadeoye ▴ 20
0
votes
2
replies
573
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
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
3
replies
735
views
Crossover design with limma
limma crossover
updated 3 months ago by 52k • written 3 months ago by ▴ 30
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
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
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
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
693
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
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
1
vote
3
replies
557
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
0
votes
5
replies
813
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 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
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
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
4
votes
3
replies
919
views
Analysis of 2*4 factorial design
limma
updated 4 months ago by 52k • written 5 months ago by • 0
2
votes
12
replies
2.0k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
5 months ago • updated 4 months ago john • 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
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 • updated 4 months ago altintas.ali • 0
2
votes
2
replies
520
views
Automatically generate contrasts from a model matrix / formula
limma
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
3
votes
3
replies
438
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
0
votes
3
replies
525
views
Need help interpreting heatmaps from limma
limma
written 5 months ago by • 0
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
665
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
1
vote
2
replies
608
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 6 months ago by ▴ 10
0
votes
0
replies
304
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
5 months ago tim.meese • 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
0
votes
2
replies
578
views
Question on performing ANOVA-like analysis using limma
limma
updated 6 months ago by 52k • written 6 months ago by • 0
17
votes
9
replies
7.4k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 6 months ago by 68k • written 8.8 years ago by ▴ 10
2
votes
1
reply
476
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 6 months ago by 68k • written 6 months ago by ▴ 10
0
votes
1
reply
1.3k
views
Unable to install/use limma
limma Bioconductor
updated 6 months ago by 68k • written 6 months ago by • 0
3
votes
3
replies
707
views
voom does not seem to properly correct for library size
limma
updated 7 months ago by 52k • written 7 months ago by ★ 4.8k
1
vote
5
replies
1.0k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 7 months ago by 52k • written 7 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
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…
Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Votes
Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
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
WEHI, Melbourne, Australia, 22 minutes ago
The Netherlands, 24 minutes ago
The city by the bay, 27 minutes ago
United States, 33 minutes ago
Seattle, WA, United States, 1 hour ago
Traffic: 637 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