Showing : limma-voom • reset
10
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5
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limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 90
10
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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
6
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4
replies
4.8k
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
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1.3k
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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
4
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4
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1.9k
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Limma-voom with external observation weights
limma limma-voom
updated 6.1 years ago by 50k • written 6.1 years ago by ★ 3.0k
3
votes
5
replies
891
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 3 months ago by ▴ 30 • written 17 months ago by • 0
3
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2
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1.2k
views
edgeR QL with voom weights
edger limma-voom voom
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 10
3
votes
14
replies
2.6k
views
limma-voom or edgeR for paired designs both within and between comparisons
edger limma-voom paired samples
7.6 years ago aec ▴ 90
2
votes
6
replies
1.7k
views
Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma limma-voom limma design matrix confounders
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 10
2
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4
replies
1.6k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 60
2
votes
5
replies
1.4k
views
Limma-Voom which of two models is correct?
limma-voom rnaseq differential gene expression
7.6 years ago Javier Gutierrez-Achury • 0
2
votes
1
reply
4.1k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 6.2 years ago by ▴ 1000 • written 6.3 years ago by ▴ 20
2
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3
replies
1.9k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
2
votes
13
replies
2.1k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
6.2 years ago • updated 6.1 years ago SPbeginner • 0
2
votes
15
replies
3.0k
views
limma: how to use pairing and adjust for covariates
limma limma-voom limma paired analysis limma contrast matrix
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
1
vote
2
replies
636
views
should smooth quantile normalization be used with limma-voom?
limma-voom smooth-quantile-normalization quantro
22 months ago raf4 ▴ 20
1
vote
8
replies
1.8k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 90
1
vote
3
replies
911
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 15 months ago by 50k • written 15 months ago by • 0
1
vote
4
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1.4k
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 6.6 years ago by 41k • written 6.6 years ago by ▴ 30
1
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6
replies
2.4k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 6.8 years ago by 50k • written 6.8 years ago by ▴ 90
1
vote
5
replies
1.8k
views
Limma: paired multifactor analysis
limma limma design matrix limma contrast matrix limma paired analysis limma-voom
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 10
1
vote
2
replies
1.7k
views
limma contrast with interaction and paired samples
limma limma-voom
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 10
0
votes
5
replies
956
views
Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
7
replies
2.5k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 6.8 years ago by ▴ 130 • written 6.8 years ago by ▴ 90
0
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3
replies
1.1k
views
upperquartile with voom
limma-voom rnaseq normalization
6.3 years ago bilcodygm • 0
0
votes
2
replies
1.2k
views
assess quality of data
rnaseq edger limma-voom
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
0
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3
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1.2k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 6.3 years ago by 50k • written 6.3 years ago by • 0
0
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3
replies
1.2k
views
quantile normalization takes into account library size?
quantile normalization limma-voom
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
0
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8
replies
2.0k
views
Limma : time course experiment with missing data
limma limma-voom
updated 12 months ago by • 0 • written 6.1 years ago by • 0
0
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4
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2.0k
views
PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom deseq2 EdgeR
updated 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 20
0
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2
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1.3k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 2.6 years ago by 50k • written 2.6 years ago by • 0
31 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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