Showing : duplicateCorrelation • reset
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
10
votes
4
replies
2.1k
views
limma-trend with random effects and/or array weights
limma-trend duplicatecorrelation arrayweights limma
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 180
8
votes
8
replies
4.4k
views
Limma: fit a model with duplicateCorrelation()
limma microarray duplicatecorrelation technical replicates linear model
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 150
8
votes
7
replies
4.7k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
6
votes
7
replies
1.8k
views
duplicateCorrelation and Pearson Correlation
limma duplicatecorrelation
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 150
6
votes
4
replies
1.7k
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
5
votes
3
replies
1.2k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
4
votes
8
replies
1.7k
views
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 8.5 years ago by 50k • written 8.5 years ago by ▴ 830
4
votes
4
replies
2.1k
views
Using duplicateCorrelation to handle replicate samples
limma duplicatecorrelation replicates
7.0 years ago rwalke13 • 0
4
votes
3
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1.4k
views
Accounting for both categorical and numerical possible confounding variables in the limmaVoom pipeline
limma limma voom duplicatecorrelation
6.8 years ago LR0306 ▴ 10
4
votes
4
replies
3.5k
views
limma - technical replicates: duplicateCorrelation() or avereps()?
limma duplicatecorrelation avereps
updated 7.6 years ago by 50k • written 7.6 years ago by ★ 3.9k
4
votes
2
replies
2.3k
views
Limma, remove batch effects and technical replicates
Limma removebatcheffect() duplicatecorrelation
7.6 years ago John ▴ 10
3
votes
2
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1.4k
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Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
2.4 years ago altintas.ali • 0
3
votes
4
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1.9k
views
Random effects with limma's camera()
limma camera duplicatecorrelation
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 30
3
votes
3
replies
2.5k
views
Duplicate Correlation with technical replicates
limma duplicatecorrelation
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by • 0
3
votes
4
replies
2.1k
views
limma-voom WithQualityWeights and duplicateCorrelation in RNA-seq
voomwithqualityweights limma voom duplicatecorrelation
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 80
2
votes
4
replies
997
views
limma: treating multiple variables as random effects in duplicateCorrelation()
limma duplicateCorrelation
updated 5.0 years ago by 50k • written 5.0 years ago by • 0
2
votes
2
replies
1.4k
views
Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
limma duplicatecorrelation arrayweights
8.6 years ago willj ▴ 30
2
votes
6
replies
2.8k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma microarray multifactorial design duplicatecorrelation model.matrix
8.4 years ago Konstantinos Yeles ▴ 80
2
votes
4
replies
1.3k
views
limma voom - time course experiment - multi level experiment
limma duplicatecorrelation limma voom
5.9 years ago • updated 5.1 years ago SPbeginner • 0
2
votes
11
replies
2.1k
views
Multi-factorial design for patient-replicates from different time points using duplicate correlation LIMMA Voom
limma limma voom duplicatecorrelation
7.1 years ago alva.james • 0
1
vote
7
replies
2.9k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
1
vote
1
reply
1.6k
views
Limma with paired samples and SVA
limma sva duplicatecorrelation estimatecellcounts
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
1
vote
6
replies
3.5k
views
Limma: advice needed for best approach for joint paired and unpaired analyses in unbalanced intervention study
limma paired unpaired duplicateCorrelation
updated 9.5 years ago by ▴ 10 • written 9.5 years ago by ★ 3.9k
1
vote
3
replies
948
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
votes
2
replies
696
views
Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
0
votes
1
reply
1.3k
views
Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
limma microarray multifactorial design duplicatecorrelation arrayweights
8.4 years ago svlachavas ▴ 830
0
votes
1
reply
942
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.4 years ago by ★ 3.9k • written 3.4 years 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
votes
0
replies
1.3k
views
Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
8.6 years ago svlachavas ▴ 830
30 results • Page 1 of 1
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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
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There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
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Bioconductor 3.19 is Released!
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