Showing : limma-voom • reset
4
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2
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783
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 5 months ago by 52k • written 5 months ago by ▴ 60
0
votes
5
replies
1.5k
views
Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
1
vote
3
replies
1.4k
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 2.2 years ago by 52k • written 2.2 years ago by ▴ 10
3
votes
5
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2.0k
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 15 months ago by ▴ 30 • written 2.5 years ago by • 0
2
votes
2
replies
970
views
should smooth quantile normalization be used with limma-voom?
limma-voom smooth-quantile-normalization quantro
2.8 years ago raf4 ▴ 30
0
votes
8
replies
2.4k
views
Limma : time course experiment with missing data
limma limma-voom
updated 2.0 years ago by • 0 • written 7.1 years ago by • 0
0
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2
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1.8k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 3.6 years ago by 52k • written 3.6 years ago by • 0
2
votes
4
replies
2.0k
views
Inconsistent result between limma/voom and DESeq2
deseq2 limma voom limma-voom rnaseq
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 60
10
votes
5
replies
3.1k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 100
0
votes
4
replies
2.6k
views
PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom deseq2 EdgeR
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 20
1
vote
8
replies
2.3k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 90
2
votes
6
replies
2.1k
views
Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma limma-voom limma design matrix confounders
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ▴ 10
4
votes
4
replies
2.5k
views
Limma-voom with external observation weights
limma limma-voom
updated 7.1 years ago by 52k • written 7.1 years ago by ★ 3.0k
2
votes
13
replies
2.7k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
7.2 years ago • updated 7.1 years ago SPbeginner • 0
0
votes
3
replies
1.6k
views
quantile normalization takes into account library size?
quantile normalization limma-voom
updated 7.2 years ago by 52k • written 7.2 years ago by • 0
2
votes
1
reply
4.9k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 7.2 years ago by ▴ 1000 • written 7.2 years ago by ▴ 20
0
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3
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1.6k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 7.2 years ago by 52k • written 7.2 years ago by • 0
0
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3
replies
1.4k
views
upperquartile with voom
limma-voom rnaseq normalization
7.3 years ago bilcodygm • 0
0
votes
2
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1.5k
views
assess quality of data
rnaseq edger limma-voom
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
5
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2
replies
1.6k
views
voomWithQualityWeights: question on min. number of replicates per group + design to use
limma edger voom voomWithQualityWeights limma-voom
updated 7.4 years ago by 52k • written 7.4 years ago by ★ 4.1k
10
votes
9
replies
2.2k
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 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
1
vote
4
replies
1.8k
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 7.6 years ago by 43k • written 7.6 years ago by ▴ 30
1
vote
6
replies
2.8k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 7.8 years ago by 52k • written 7.8 years ago by ▴ 90
0
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7
replies
3.0k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.8 years ago by ▴ 130 • written 7.8 years ago by ▴ 90
6
votes
4
replies
5.5k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 8.1 years ago by ★ 7.9k • written 8.1 years ago by ▴ 10
2
votes
15
replies
3.8k
views
limma: how to use pairing and adjust for covariates
limma limma-voom limma paired analysis limma contrast matrix
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
2
votes
3
replies
2.3k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
3
votes
2
replies
1.5k
views
edgeR QL with voom weights
edger limma-voom voom
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
1
vote
2
replies
2.0k
views
limma contrast with interaction and paired samples
limma limma-voom
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
1
vote
5
replies
2.2k
views
Limma: paired multifactor analysis
limma limma design matrix limma contrast matrix limma paired analysis limma-voom
updated 8.2 years ago by 52k • written 8.2 years ago by ▴ 10
2
votes
5
replies
1.7k
views
Limma-Voom which of two models is correct?
limma-voom rnaseq differential gene expression
8.6 years ago Javier Gutierrez-Achury • 0
3
votes
14
replies
3.2k
views
limma-voom or edgeR for paired designs both within and between comparisons
edger limma-voom paired samples
8.6 years ago aec ▴ 90
32 results • Page 1 of 1
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Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply Here are the count plots for one example CD44: normalised: ![enter image description here][1] unnormalised: !…
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Votes
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
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