Showing : voom • reset
23
votes
11
replies
18k
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 8.2 years ago by 50k • written 8.2 years ago by ▴ 50
21
votes
5
replies
14k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 9.0 years ago by 50k • written 9.9 years ago by ▴ 190
11
votes
8
replies
8.5k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 70
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
16
votes
5
replies
7.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 120
5
votes
2
replies
7.2k
views
Ballgown vs (voom,edgeR,DESeq,limma)
limma rnaseq differential expression voom
updated 9.3 years ago by ▴ 210 • written 9.3 years ago by ▴ 50
25
votes
9
replies
6.8k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 9.2 years ago by 50k • written 9.2 years ago by ▴ 40
8
votes
8
replies
6.7k
views
Voom transformation from counts and normalization to negative values
rnaseq voom limma tcga statistics
updated 5.6 years ago by ★ 7.9k • written 5.6 years ago by ▴ 60
13
votes
21
replies
6.0k
views
modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
limma voom hurdle single cell
8.6 years ago osa.zuta ▴ 40
1
vote
13
replies
5.9k
views
edgeR vs voom
edger voom limma
8.8 years ago • updated 8.7 years ago dongamit123 ▴ 20
5
votes
9
replies
5.9k
views
Voom: need at least two non-NA values to interpolate
limma voom voom rsem fpkm
7.6 years ago komal.rathi ▴ 120
3
votes
6
replies
5.4k
views
RNAseq, what to do if you have no replicates in voom-limma
limma voom edger
updated 7.6 years ago by ▴ 20 • written 8.8 years ago by ▴ 80
9
votes
9
replies
5.2k
views
Voom on TCGA data shifts count distributions towards negative values
voom TCGA RNAseq
9.4 years ago paola.ostano ▴ 10
0
votes
2
replies
5.2k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.2 years ago RJM • 0
6
votes
13
replies
5.1k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 21 months ago by 50k • written 3.7 years ago by ▴ 60
6
votes
4
replies
4.7k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 10
10
votes
6
replies
4.7k
views
Bootstrap confidence intervals on RNA-seq expression from Kallisto
rnaseq deseq2 edger voom limma
updated 6.6 years ago by ▴ 100 • written 8.9 years ago by 21k
12
votes
4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 5.3 years ago by 50k • written 6.9 years ago by ▴ 30
10
votes
4
replies
4.4k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.7 years ago by 50k • written 7.7 years ago by ▴ 110
7
votes
3
replies
4.3k
views
VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
r limma voom vsn
updated 17 months ago by 50k • written 5.1 years ago by ▴ 70
6
votes
5
replies
4.2k
views
voom + removeBatchEffect + gene clustering
voom limma clustering removebatcheffect() batch effect
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 10
6
votes
4
replies
4.1k
views
RSEM expected counts to limma-voom
limma voom rsem
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 90
2
votes
1
reply
4.0k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 6.2 years ago by ▴ 1000 • written 6.2 years ago by ▴ 20
3
votes
12
replies
3.8k
views
Problem about use of TCGA rna-seq rsem gene results for regularized cox regression modeling
tcga rnaseq glmnet voom deseq2
7.1 years ago panagiotis.mokos ▴ 40
1
vote
12
replies
3.7k
views
Limma-voom design for multifactorial RNA-seq experiment
limma voom multiple factor design limma voom
8.4 years ago oliver.selmoni • 0
10
votes
13
replies
3.6k
views
DE for genes with very low counts using limma.
limma voom limma-trend
updated 7.5 years ago by 50k • written 7.5 years ago by ▴ 170
5
votes
2
replies
3.4k
views
Differences when using voom on a design with or without intercept
limma voom linear model
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 20
2
votes
7
replies
3.4k
views
limma+voom question for effect across multiple tissues
limma voom
updated 9.5 years ago by ★ 28k • written 9.5 years ago by ▴ 10
4
votes
2
replies
3.3k
views
PCA for voom normalized RNAseq data
voom pca
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 120
2
votes
6
replies
3.3k
views
voom/limma contrast for comparing one level against base-line
limma voom contrast
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 80
4
votes
8
replies
3.2k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 9.1 years ago by ▴ 1000 • written 9.2 years ago by ▴ 20
3
votes
3
replies
3.2k
views
Voom without design matrix
limma voom
9.3 years ago Ninni Nahm ▴ 50
3
votes
6
replies
3.1k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma voom rnaseq model.matrix intercept
updated 4.4 years ago by 50k • written 4.4 years ago by ▴ 30
4
votes
2
replies
3.1k
views
limma-voom for miRNA seq
limma voom
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 90
3
votes
6
replies
3.1k
views
Pool Single-cells: Analysis
deseq2 single cell limma voom
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 90
13
votes
2
replies
3.1k
views
voom with combat
limma voom combat batch effect
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 10
0
votes
6
replies
3.1k
views
How to use RUVseq with voom-limma for differential expression analysis?
ruvseq limma voom
updated 7.6 years ago by ▴ 950 • written 7.7 years ago by • 0
4
votes
2
replies
3.0k
views
applying voom + limma to a block factor design in RNA-seq experiment
limma voom
7.0 years ago jfertaj ▴ 30
3
votes
10
replies
2.7k
views
Limma voom RNA-seq analysis with both categorical and continuous confounders
limma voom
updated 6.3 years ago by 50k • written 6.3 years ago by • 0
8
votes
3
replies
2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.6 years ago lanhuong ▴ 20
2
votes
4
replies
2.7k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 24 months ago by 50k • written 24 months ago by ▴ 20
1
vote
6
replies
2.6k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.4 years ago by ▴ 10
4
votes
6
replies
2.6k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 3.9 years ago by 50k • written 3.9 years ago by ▴ 10
4
votes
4
replies
2.6k
views
Expression profile from $E from Voom
Voom $EList
updated 6.6 years ago by ★ 13k • written 6.6 years ago by ▴ 60
4
votes
10
replies
2.6k
views
Effects of continuous variable with adjustment for gender
edger limma voom
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 10
8
votes
2
replies
2.5k
views
limma-voom when testing differential expression of a subset of genes.
limma voom differential gene expression
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 40
7
votes
5
replies
2.4k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 10
0
votes
4
replies
2.4k
views
Normalization and transformation of RNA-seq raw data for regularized linear regression models
rnaseq glmnet limma voom deseq2
7.1 years ago panagiotis.mokos ▴ 40
3
votes
5
replies
2.4k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
2.4 years ago Tyler Sagendorf ▴ 10
3
votes
6
replies
2.4k
views
block design to test two factors with limma
limma voom
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 30
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Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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