Showing : limma-voom • reset
4
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2
replies
369
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 2 days ago by 51k • written 2 days ago by ▴ 50
0
votes
5
replies
1.3k
views
Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 20 months ago by 51k • written 21 months ago by • 0
1
vote
3
replies
1.2k
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 21 months ago by 51k • written 21 months ago by ▴ 10
3
votes
5
replies
1.5k
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 10 months ago by ▴ 30 • written 2.0 years ago by • 0
2
votes
2
replies
875
views
should smooth quantile normalization be used with limma-voom?
limma-voom smooth-quantile-normalization quantro
2.4 years ago raf4 ▴ 30
0
votes
8
replies
2.3k
views
Limma : time course experiment with missing data
limma limma-voom
updated 19 months ago by • 0 • written 6.7 years ago by • 0
0
votes
2
replies
1.6k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 3.2 years ago by 51k • written 3.2 years ago by • 0
2
votes
4
replies
1.8k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 6.0 years ago by 51k • written 6.0 years ago by ▴ 60
10
votes
5
replies
2.9k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 6.1 years ago by 51k • written 6.1 years ago by ▴ 100
0
votes
4
replies
2.3k
views
PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom deseq2 EdgeR
updated 6.1 years ago by ★ 13k • written 6.1 years ago by ▴ 20
1
vote
8
replies
2.1k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 6.2 years ago by ★ 28k • written 6.2 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 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 10
4
votes
4
replies
2.2k
views
Limma-voom with external observation weights
limma limma-voom
updated 6.7 years ago by 51k • written 6.7 years ago by ★ 3.0k
2
votes
13
replies
2.4k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
6.7 years ago SPbeginner • 0
0
votes
3
replies
1.4k
views
quantile normalization takes into account library size?
quantile normalization limma-voom
updated 6.8 years ago by 51k • written 6.8 years ago by • 0
2
votes
1
reply
4.5k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 6.8 years ago by ▴ 1000 • written 6.8 years ago by ▴ 20
0
votes
3
replies
1.4k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 6.8 years ago by 51k • written 6.8 years ago by • 0
0
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3
replies
1.2k
views
upperquartile with voom
limma-voom rnaseq normalization
6.8 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 6.8 years ago by 42k • written 6.8 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 7.0 years ago by 51k • written 7.0 years ago by ★ 4.1k
10
votes
9
replies
2.0k
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 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
1
vote
4
replies
1.6k
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 7.2 years ago by 42k • written 7.2 years ago by ▴ 30
1
vote
6
replies
2.6k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 7.3 years ago by 51k • written 7.3 years ago by ▴ 90
0
votes
7
replies
2.8k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by ▴ 90
6
votes
4
replies
5.2k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
2
votes
15
replies
3.4k
views
limma: how to use pairing and adjust for covariates
limma limma-voom limma paired analysis limma contrast matrix
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 10
2
votes
3
replies
2.1k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
3
votes
2
replies
1.4k
views
edgeR QL with voom weights
edger limma-voom voom
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
1
vote
2
replies
1.9k
views
limma contrast with interaction and paired samples
limma limma-voom
updated 7.8 years ago by ★ 28k • written 7.8 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 7.8 years ago by 51k • written 7.8 years ago by ▴ 10
2
votes
5
replies
1.5k
views
Limma-Voom which of two models is correct?
limma-voom rnaseq differential gene expression
8.1 years ago Javier Gutierrez-Achury • 0
3
votes
14
replies
2.9k
views
limma-voom or edgeR for paired designs both within and between comparisons
edger limma-voom paired samples
8.2 years ago aec ▴ 90
32 results • Page 1 of 1
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Answer: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
Comment: Unlocking Potential: NURS FPX Strategies and Insights by efsane_kral2000 • 0
https://www.hayalsohbet.net https://www.yerlichat.com https://www.yerlichat.net https://www.mavisim.net https://www.hayalchat.com http…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Answer: Differene between the Wald and LRT test for time-series gene expression data by James W. MacDonald 67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
Votes
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Allele frequencies for ALL alleles of one SNP ?
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Using Affymetrix Custom Array
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Popular Question to Fred Hutch (Recruiting) ▴ 40
Scholar to Gordon Smyth 51k
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