Showing : voom • reset
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
24
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
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
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
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
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
11
votes
3
replies
1.7k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.8 years ago by ★ 3.3k • written 7.8 years ago by ▴ 110
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
10
votes
9
replies
1.7k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom voom limma rna-seq
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
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
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
10
votes
4
replies
4.4k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 110
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
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
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
8
votes
5
replies
2.5k
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
8
votes
3
replies
2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.6 years ago lanhuong ▴ 20
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 5.2 years ago by ▴ 70
7
votes
2
replies
771
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 7.2 years ago by 50k • written 7.2 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
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
1.7k
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
6
votes
5
replies
1.5k
views
t-statistic from various limma-approaches does not follow the theoretical distribution
limma t-statistic voom voomwithqualityweights robust regression
5.4 years ago brynedal ▴ 40
6
votes
4
replies
1.4k
views
Combining newer/older RNAseq data, batch correcting
rnaseq limma sva batch effect voom
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
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
4.7k
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
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
5
votes
3
replies
1.7k
views
Support for offsets in cpm and voom functions?
edgeR cpm voom limma
8.6 years ago Ryan C. Thompson ★ 7.9k
5
votes
2
replies
1.3k
views
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma edger voom voomWithQualityWeights limma-voom
updated 6.4 years ago by 50k • written 6.4 years ago by ★ 3.9k
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
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
5
votes
7
replies
2.2k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 20
5
votes
2
replies
535
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
5
votes
6
replies
1.7k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
21 months ago Yang Shi ▴ 10
5
votes
3
replies
692
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 6 months ago by 50k • written 6 months ago by ▴ 180
4
votes
7
replies
1.5k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 4.4 years ago by 50k • written 4.4 years ago by ▴ 50
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
8
replies
3.2k
views
Visualising effects of observation/sample weights in differential expression analysis
limma voom sva edgeR
updated 9.2 years ago by ▴ 1000 • written 9.2 years ago by ▴ 20
4
votes
5
replies
947
views
Defining the design for a complicated multi-level experiment in Limma
limma RNASeq R voom
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 60
4
votes
6
replies
2.7k
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
972
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
4
votes
2
replies
1.5k
views
Voom: estimation of mean-variance relationship with gene expression data normalized with methods other than cpm
limma voom
updated 8.0 years ago by 50k • written 8.0 years ago by • 0
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
4
votes
2
replies
3.0k
views
applying voom + limma to a block factor design in RNA-seq experiment
limma voom
7.1 years ago • updated 7.0 years ago jfertaj ▴ 30
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
4
votes
10
replies
2.0k
views
Subject: Strange glitch in Voom curve resulting from batch effects
limma voom batcheffect covariate
updated 7.0 years ago by 50k • written 7.0 years ago by ▴ 20
4
votes
3
replies
1.1k
views
Where is the source code for qAbundanceDist?
voom
updated 7.6 years ago by 50k • written 7.6 years ago by ▴ 70
4
votes
2
replies
3.4k
views
PCA for voom normalized RNAseq data
voom pca
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 120
50 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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