Showing : limma-voom • reset
6
votes
4
replies
4.7k
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
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 6.2 years ago by ▴ 20
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
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
10
votes
5
replies
2.5k
views
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
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
1
vote
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
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
6.1 years ago SPbeginner • 0
0
votes
4
replies
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
votes
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
2
votes
3
replies
1.8k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
4
votes
4
replies
1.8k
views
Limma-voom with external observation weights
limma limma-voom
updated 6.1 years ago by 50k • written 6.1 years ago by ★ 3.0k
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
5
replies
1.7k
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
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
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 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
2
votes
4
replies
1.5k
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
1
vote
4
replies
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
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
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
0
votes
2
replies
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
0
votes
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
votes
3
replies
1.2k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
3
votes
2
replies
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
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
votes
3
replies
1.1k
views
upperquartile with voom
limma-voom rnaseq normalization
6.3 years ago bilcodygm • 0
0
votes
5
replies
939
views
Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 13 months ago by 50k • written 14 months ago by • 0
1
vote
3
replies
889
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
3
votes
5
replies
861
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
1
vote
2
replies
629
views
should smooth quantile normalization be used with limma-voom?
limma-voom smooth-quantile-normalization quantro
21 months ago raf4 ▴ 20
31 results • Page 1 of 1
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Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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