Showing : Limma • reset
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
32
votes
0
replies
42k
views
limma moderated t-statistics and B-statistics
Microarray limma
20.5 years ago • updated 4.4 years ago Gordon Smyth 52k
28
votes
8
replies
13k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 7.5 years ago by 52k • written 10.0 years ago by ▴ 160
25
votes
7
replies
12k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 20
25
votes
9
replies
7.9k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 10.2 years ago by 52k • written 10.2 years ago by ▴ 40
24
votes
11
replies
20k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 9.2 years ago by 52k • written 9.2 years ago by ▴ 50
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring limma
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ▴ 370
22
votes
4
replies
11k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 9.8 years ago by 52k • written 9.8 years ago by ▴ 840
22
votes
8
replies
5.1k
views
Limma camera function never gives any differentially expressed gene sets
limma
updated 7.6 years ago by • 0 • written 9.7 years ago by ▴ 420
21
votes
5
replies
17k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 9.9 years ago by 52k • written 10.9 years ago by ▴ 190
20
votes
18
replies
5.6k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 9.5 years ago by ▴ 870 • written 9.5 years ago by ▴ 840
19
votes
10
replies
4.8k
views
Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma romer
updated 9.6 years ago by 52k • written 9.6 years ago by ▴ 40
18
votes
37
replies
18k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
9.8 years ago • updated 9.7 years ago svlachavas ▴ 840
18
votes
3
replies
3.9k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma voomwithqualityweights gene set analysis
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 80
17
votes
5
replies
6.3k
views
limma voom Mean-variance trend plot: x-axis?
limma
5.9 years ago AS ▴ 70
17
votes
9
replies
7.5k
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
17
votes
14
replies
49k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.8 years ago by • 0 • written 7.7 years ago by ▴ 20
16
votes
13
replies
5.6k
views
Camera and ROAST
limma
updated 7.3 years ago by 52k • written 7.3 years ago by ▴ 30
16
votes
0
replies
4.5k
views
simultaneous use of robust and weighting methods in limma
limma robust arrayWeights
11.3 years ago • updated 8.8 years ago Gordon Smyth 52k
16
votes
6
replies
6.9k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma goana
updated 9.7 years ago by 52k • written 9.7 years ago by ▴ 20
16
votes
6
replies
3.8k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 8.6 years ago by ▴ 90 • written 8.6 years ago by ▴ 180
16
votes
5
replies
8.1k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 9.4 years ago by 52k • written 9.4 years ago by ▴ 120
15
votes
17
replies
2.6k
views
Why p value inconsistent when using different number of pathway score?
limma
11 months ago • updated 10 months ago Chris ▴ 20
15
votes
23
replies
3.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
12 months ago • updated 11 months ago Chris ▴ 20
15
votes
14
replies
4.1k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 10.1 years ago by 21k • written 10.2 years ago by ▴ 340
15
votes
4
replies
3.4k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 8.7 years ago by ★ 7.9k • written 8.7 years ago by ▴ 130
14
votes
16
replies
3.2k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 10
14
votes
12
replies
11k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 8.6 years ago by ★ 13k • written 8.6 years ago by ▴ 30
14
votes
9
replies
4.4k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 7.2 years ago by ▴ 130 • written 8.9 years ago by ▴ 80
14
votes
16
replies
3.4k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
8.8 years ago giroudpaul ▴ 40
14
votes
2
replies
3.6k
views
voom with combat
limma voom combat batch effect
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 10
13
votes
3
replies
14k
views
Understanding contrasts limma
limma design and contrast matrix
updated 9.5 years ago by ★ 28k • written 9.5 years ago by ▴ 60
13
votes
21
replies
7.1k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
9.6 years ago • updated 9.5 years ago osa.zuta ▴ 40
13
votes
9
replies
9.0k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
10.0 years ago svlachavas ▴ 840
13
votes
2
replies
7.1k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma covariate continuous categorical adjustment
updated 9.7 years ago by 52k • written 9.7 years ago by • 0
12
votes
6
replies
1.8k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
12
votes
3
replies
12k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot limma fdr
7.7 years ago • updated 4.4 years ago tcalvo ▴ 100
12
votes
9
replies
4.2k
views
Limma residuals matrix
limma
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 20
12
votes
18
replies
6.6k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 4.0 years ago by 52k • written 4.5 years ago by ▴ 10
12
votes
4
replies
5.0k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 6.2 years ago by 52k • written 7.8 years ago by ▴ 30
12
votes
20
replies
2.6k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 9.6 years ago by ★ 28k • written 9.6 years ago by ▴ 840
12
votes
5
replies
14k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 7.7 years ago by 52k • written 16.3 years ago by ▴ 190
11
votes
6
replies
4.5k
views
Log fold change on Limma
limma multiple factor design
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 20
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
11
votes
9
replies
1.9k
views
Correlation of a Linear Variable
limma limma design matrix
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 370
11
votes
9
replies
5.3k
views
How to remove more than two batches in my data-sets
limma RNAseq removebatcheffect()
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 30
11
votes
4
replies
2.4k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 18 months ago by 52k • written 6.1 years ago by • 0
11
votes
16
replies
2.2k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 9.5 years ago by 68k • written 9.5 years ago by ▴ 840
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 80
11
votes
3
replies
2.1k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 8.7 years ago by ★ 3.4k • written 8.7 years ago by ▴ 110
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
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…
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}
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