Showing : VOOM • reset
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
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
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
2
votes
3
replies
1.2k
views
voom command broken in limma_3.34.5?
limma voom
updated 6.3 years ago by 50k • written 6.3 years ago by • 0
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
11
votes
3
replies
1.7k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.7 years ago by ★ 3.2k • written 7.7 years ago by ▴ 110
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
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
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
3
votes
4
replies
2.0k
views
Voom nornalization lowess span
voom normalization
updated 8.1 years ago by 50k • written 8.1 years ago by ▴ 50
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
10
replies
2.0k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
20 months ago • updated 19 months ago Hilary ▴ 30
3
votes
5
replies
2.0k
views
PCA of voom weight values
limma voom rnaseq
updated 9.1 years ago by 50k • written 9.1 years ago by ▴ 120
0
votes
4
replies
1.0k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 620
3
votes
6
replies
1.7k
views
paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 4.1 years ago by 50k • written 4.1 years ago by • 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
5
votes
2
replies
512
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
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
2
votes
2
replies
1.1k
views
Different results from limma depending on whether or not I have an intercept term in my model
limma lmfit voom limma design matrix voomwithqualityweights
updated 5.3 years ago by 50k • written 5.3 years ago by ▴ 10
3
votes
3
replies
3.2k
views
Voom without design matrix
limma voom
9.3 years ago Ninni Nahm ▴ 50
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
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
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
21
votes
5
replies
14k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma voom
updated 8.9 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
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
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
0
votes
5
replies
1.2k
views
Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
6.4 years ago scanchi • 0
0
votes
2
replies
1.1k
views
Subsetting an EList Object doesn't subset $sample.weights
voom EList limma
updated 6.3 years ago by 50k • written 6.3 years ago by ▴ 170
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
2
votes
6
replies
2.0k
views
Three way-interaction on voom (limma) data, including a factor with > 2 levels
RNASeq limma voom anova
updated 2.1 years ago by ▴ 90 • written 6.8 years ago by ▴ 90
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
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
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
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
2
votes
7
replies
1.3k
views
Weird results (ribosomal proteins / Y-linked genes) in limma/voom
limma voom rnaseq
updated 7.5 years ago by 50k • written 7.5 years ago by ▴ 10
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
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
3
votes
2
replies
2.1k
views
Paired Test - Design Matrix and Contrast Matrix Voom and Limma
limma voom paired samples
updated 6.4 years ago by 50k • written 6.4 years ago by • 0
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
13
votes
2
replies
3.1k
views
voom with combat
limma voom combat batch effect
updated 7.7 years ago by 50k • written 7.7 years ago by ▴ 10
4
votes
3
replies
2.2k
views
mean-variance corrected data from voom
limma voom
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 20
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
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
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
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
8
votes
3
replies
2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.6 years ago lanhuong ▴ 20
4
votes
3
replies
1.6k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 4.6 years ago by ▴ 110 • written 4.8 years ago by ▴ 50
0
votes
2
replies
1.1k
views
Further analysis of gene expression data
limma voom rnaseq
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 60
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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