Showing : limma-voom • reset
4
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2
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572
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 8 weeks ago by 52k • written 9 weeks ago by ▴ 50
0
votes
5
replies
1.4k
views
Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 22 months ago by 52k • written 23 months ago by • 0
1
vote
3
replies
1.3k
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 24 months ago by 52k • written 24 months ago by ▴ 10
3
votes
5
replies
1.7k
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 12 months ago by ▴ 30 • written 2.2 years ago by • 0
2
votes
2
replies
908
views
should smooth quantile normalization be used with limma-voom?
limma-voom smooth-quantile-normalization quantro
2.5 years ago raf4 ▴ 30
0
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8
replies
2.3k
views
Limma : time course experiment with missing data
limma limma-voom
updated 21 months ago by • 0 • written 6.8 years ago by • 0
0
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2
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1.7k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
2
votes
4
replies
1.9k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 6.1 years ago by 52k • written 6.1 years ago by ▴ 60
10
votes
5
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3.0k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 100
0
votes
4
replies
2.4k
views
PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom deseq2 EdgeR
updated 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 20
1
vote
8
replies
2.2k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 90
2
votes
6
replies
1.9k
views
Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma limma-voom limma design matrix confounders
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 10
4
votes
4
replies
2.2k
views
Limma-voom with external observation weights
limma limma-voom
updated 6.9 years ago by 52k • written 6.9 years ago by ★ 3.0k
2
votes
13
replies
2.5k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
6.9 years ago SPbeginner • 0
0
votes
3
replies
1.4k
views
quantile normalization takes into account library size?
quantile normalization limma-voom
updated 6.9 years ago by 52k • written 6.9 years ago by • 0
2
votes
1
reply
4.6k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 7.0 years ago by ▴ 1000 • written 7.0 years ago by ▴ 20
0
votes
3
replies
1.5k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 7.0 years ago by 52k • written 7.0 years ago by • 0
0
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3
replies
1.3k
views
upperquartile with voom
limma-voom rnaseq normalization
7.0 years ago bilcodygm • 0
0
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2
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1.4k
views
assess quality of data
rnaseq edger limma-voom
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
5
votes
2
replies
1.5k
views
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma edger voom voomWithQualityWeights limma-voom
updated 7.2 years ago by 52k • written 7.2 years ago by ★ 4.1k
10
votes
9
replies
2.1k
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 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
1
vote
4
replies
1.7k
views
Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
salmon tximport limma-voom
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 30
1
vote
6
replies
2.6k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 90
0
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7
replies
2.8k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.5 years ago by ▴ 130 • written 7.5 years ago by ▴ 90
6
votes
4
replies
5.3k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by ▴ 10
2
votes
15
replies
3.5k
views
limma: how to use pairing and adjust for covariates
limma limma-voom limma paired analysis limma contrast matrix
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
2
votes
3
replies
2.1k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
3
votes
2
replies
1.4k
views
edgeR QL with voom weights
edger limma-voom voom
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
1
vote
2
replies
1.9k
views
limma contrast with interaction and paired samples
limma limma-voom
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
1
vote
5
replies
2.0k
views
Limma: paired multifactor analysis
limma limma design matrix limma contrast matrix limma paired analysis limma-voom
updated 8.0 years ago by 52k • written 8.0 years ago by ▴ 10
2
votes
5
replies
1.6k
views
Limma-Voom which of two models is correct?
limma-voom rnaseq differential gene expression
8.3 years ago Javier Gutierrez-Achury • 0
3
votes
14
replies
3.0k
views
limma-voom or edgeR for paired designs both within and between comparisons
edger limma-voom paired samples
8.3 years ago aec ▴ 90
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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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