Showing : Limma • reset
34
votes
11
replies
43k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.5 years ago by ▴ 270
32
votes
0
replies
43k
views
limma moderated t-statistics and B-statistics
Microarray limma
20.7 years ago • updated 4.6 years ago Gordon Smyth 52k
28
votes
8
replies
13k
views
Removing continuous covariate effects in limma analysis
limma microarray
updated 7.7 years ago by 52k • written 10.1 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 7.6 years ago by 52k • written 7.6 years ago by ▴ 20
25
votes
9
replies
8.0k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 10.3 years ago by 52k • written 10.3 years ago by ▴ 40
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring limma
updated 10.0 years ago by ▴ 20 • written 10.1 years ago by ▴ 370
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 9.3 years ago by 52k • written 9.3 years ago by ▴ 50
22
votes
8
replies
5.2k
views
Limma camera function never gives any differentially expressed gene sets
limma
updated 7.8 years ago by • 0 • written 9.9 years ago by ▴ 420
22
votes
4
replies
12k
views
Correct assumptions of using limma moderated t-test
limma statistical inference variance test bioconductor
updated 10.0 years ago by 52k • written 10.0 years ago by ▴ 840
21
votes
5
replies
17k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 10.0 years ago by 52k • written 11.0 years ago by ▴ 190
20
votes
18
replies
5.8k
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 9.6 years ago by ▴ 870 • written 9.6 years ago by ▴ 840
19
votes
10
replies
4.9k
views
Do the outputs of Limma's competitive gene set methods (camera, romer) require a mutliple testing correction?
limma romer
updated 9.7 years ago by 52k • written 9.7 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
10.0 years ago • updated 9.8 years ago svlachavas ▴ 840
18
votes
3
replies
4.0k
views
cameraPR vs geneSetTest and ROAST/CAMERA in general
limma voomwithqualityweights gene set analysis
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 80
17
votes
9
replies
7.7k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 8 months ago by 68k • written 9.0 years ago by ▴ 10
17
votes
14
replies
51k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 2.9 years ago by • 0 • written 7.8 years ago by ▴ 20
17
votes
5
replies
6.6k
views
limma voom Mean-variance trend plot: x-axis?
limma
6.1 years ago AS ▴ 70
16
votes
0
replies
4.7k
views
simultaneous use of robust and weighting methods in limma
limma robust arrayWeights
11.4 years ago • updated 9.0 years ago Gordon Smyth 52k
16
votes
6
replies
3.9k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 8.8 years ago by ▴ 90 • written 8.8 years ago by ▴ 180
16
votes
6
replies
7.0k
views
goana limma- extract list of DE genes and genes in the enriched GO terms?
limma goana
updated 9.9 years ago by 52k • written 9.9 years ago by ▴ 20
16
votes
5
replies
8.3k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 9.5 years ago by 52k • written 9.5 years ago by ▴ 120
16
votes
13
replies
5.8k
views
Camera and ROAST
limma
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 30
15
votes
17
replies
2.9k
views
Why p value inconsistent when using different number of pathway score?
limma
13 months ago • updated 12 months ago Chris ▴ 20
15
votes
23
replies
4.4k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
13 months ago • updated 12 months ago Chris ▴ 20
15
votes
14
replies
4.3k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 10.3 years ago by 21k • written 10.3 years ago by ▴ 340
15
votes
4
replies
3.5k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 130
14
votes
16
replies
3.3k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 10
14
votes
9
replies
4.5k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 7.3 years ago by ▴ 130 • written 9.1 years ago by ▴ 80
14
votes
16
replies
3.5k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
9.0 years ago giroudpaul ▴ 40
14
votes
3
replies
15k
views
Understanding contrasts limma
limma design and contrast matrix
updated 9.6 years ago by ★ 28k • written 9.6 years ago by ▴ 60
14
votes
2
replies
3.7k
views
voom with combat
limma voom combat batch effect
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 10
14
votes
12
replies
11k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 8.8 years ago by ★ 13k • written 8.8 years ago by ▴ 30
13
votes
2
replies
7.2k
views
Using limma when continuous and categorical confounders are present at the same time (e.g.age, gender)
limma covariate continuous categorical adjustment
updated 9.8 years ago by 52k • written 9.8 years ago by • 0
13
votes
9
replies
9.1k
views
Appropriate use of the function treat of the limma package
limma treat microarray bioconductor
10.2 years ago svlachavas ▴ 840
13
votes
21
replies
7.2k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
9.7 years ago osa.zuta ▴ 40
12
votes
5
replies
14k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 7.8 years ago by 52k • written 16.5 years ago by ▴ 190
12
votes
6
replies
1.9k
views
Testing for DE genes
affymetrix microarrays limma differential gene expression
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
12
votes
3
replies
13k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot limma fdr
7.8 years ago • updated 4.5 years ago tcalvo ▴ 100
12
votes
18
replies
6.9k
views
What is the correct use of removeBatchEffect's design parameter
deseq2 limma
updated 4.2 years ago by 52k • written 4.7 years ago by ▴ 10
12
votes
4
replies
5.1k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 6.4 years ago by 52k • written 8.0 years ago by ▴ 30
12
votes
20
replies
2.7k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 9.7 years ago by ★ 28k • written 9.7 years ago by ▴ 840
12
votes
9
replies
4.4k
views
Limma residuals matrix
limma
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 20
11
votes
6
replies
4.6k
views
Log fold change on Limma
limma multiple factor design
updated 9.9 years ago by ★ 13k • written 9.9 years ago by ▴ 20
11
votes
4
replies
3.5k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 days ago by 52k • written 17 months ago by • 0
11
votes
9
replies
2.0k
views
Correlation of a Linear Variable
limma limma design matrix
updated 10.1 years ago by 68k • written 10.1 years ago by ▴ 370
11
votes
9
replies
5.5k
views
How to remove more than two batches in my data-sets
limma RNAseq removebatcheffect()
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 30
11
votes
4
replies
2.4k
views
LIMMA dupcor() function time issue.
limma microarray block
updated 20 months ago by 52k • written 6.3 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 9.7 years ago by 68k • written 9.7 years ago by ▴ 840
11
votes
3
replies
2.1k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 8.8 years ago by ★ 3.4k • written 8.8 years ago by ▴ 110
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.7 years ago by 52k • written 7.7 years ago by ▴ 80
50 results • Page 1 of 1
Recent ...
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Comment: FlowSOM is unable to create Output by EvangelinePope • 0
I will remember it, Thank you so much for sharing.
Answer: Limma suqeezeVar by Gordon Smyth 52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
Comment: Discrepancies in normalised count data vs unnormalised by swbarnes2 ★ 1.4k
Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…
Comment: Can't install BioC packages (and manager) behind firewall by Marcel Ramos 700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa by Alejandro • 0
Dear Gordon, Thank you very much!
Votes
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
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