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
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 ▴ 180
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
1
vote
13
replies
6.0k
views
edgeR vs voom
edger voom limma
8.8 years ago dongamit123 ▴ 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
3
votes
11
replies
2.1k
views
Limma Voom and quadratic regression
limma voom
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 140
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 8.3 years ago by 50k • written 8.3 years ago by ▴ 50
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
3
votes
10
replies
2.8k
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
1
vote
10
replies
2.0k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
20 months ago Hilary ▴ 30
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
2
votes
9
replies
2.2k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
22 months ago Peipei • 0
25
votes
9
replies
6.8k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 40
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
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
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
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
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
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
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
3
votes
7
replies
1.3k
views
Weird results (ribosomal proteins / Y-linked genes) in limma/voom
limma voom rnaseq
updated 7.6 years ago by 50k • written 7.6 years ago by ▴ 10
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
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
2
votes
6
replies
2.1k
views
Three way-interaction on voom (limma) data, including a factor with > 2 levels
RNASeq limma voom anova
updated 2.2 years ago by ▴ 90 • written 6.8 years ago by ▴ 90
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
0
votes
6
replies
3.1k
views
How to use RUVseq with voom-limma for differential expression analysis?
ruvseq limma voom
updated 7.7 years ago by ▴ 950 • written 7.7 years ago by • 0
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
3
votes
6
replies
3.2k
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
1
vote
6
replies
2.7k
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 7.5 years ago by ▴ 10
3
votes
6
replies
5.5k
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
3
votes
6
replies
1.1k
views
Paired RNA-seq experiment with 3 factors using duplicateCorrelation
paired samples multiple factor design limma voom
updated 7.5 years ago by 50k • written 7.5 years ago by ▴ 90
3
votes
6
replies
2.2k
views
Controlling numerical covariates: differential gene expression with limma voom
limma voom differential gene expression rnaseq R
updated 5.4 years ago by ▴ 270 • written 5.4 years ago by • 0
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
6
replies
1.4k
views
Improve limma-voom trend fit to noisy data
limma voom
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 70
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
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
3
votes
6
replies
3.1k
views
Pool Single-cells: Analysis
deseq2 single cell limma voom
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 90
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
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
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
1
vote
5
replies
1.4k
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
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
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 10.0 years ago by ▴ 190
1
vote
5
replies
1.3k
views
Limma-voom read count analysis
Differentially methylated CpG's Limma Voom Read Count
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
1
vote
5
replies
1.3k
views
Time course experiment using limma with voom
limma voom RNA Seq Time-course experiments
updated 4.9 years ago by ★ 28k • written 4.9 years 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
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
4
votes
5
replies
949
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
Sorry, for questions about statistical analysis plan and interpretation of results, I recommend to work with a local statistician or someon…
Answer: Fold change calculation in Diffbind vs. DESEQ2? by Michael Love 41k
There was a recent DiffBind question on the support site that noticed the same thing, try searching recent DiffBind posts.
Answer: Timecourse RNASeq analysis by Michael Love 41k
There are many choices for time course, and we have an example in our workflow (rnaseqGene). Otherwise, I recommend to consult a local …
Answer: Padj "NA" with thousands of low count although the raw read counts are quite lar by Michael Love 41k
You can either turn off independent filtering in `results` or use `ihw` see the vignette.
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Thanks Gordon for a detail guide! You have a great memory of time. GSVA also do differential express at pathway level (https://bioconductor…
Votes
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Awards • All
Centurion to Chris • 0
Commentator to Leonard Goldstein ▴ 200
Popular Question to Matthew Ritchie ▴ 1000
Scholar to alserg ▴ 260
Popular Question to bioinf ▴ 10
Locations • All
United States, 1 minute ago
St Louis, MO, 3 minutes ago
France, 19 minutes ago
Italy, 28 minutes ago
UPF, Barcelona, Spain, 40 minutes ago
Traffic: 794 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6