Showing : duplicatecorrelation • reset
10
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5
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2.5k
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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
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 ▴ 170
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 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 50
6
votes
7
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1.8k
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duplicateCorrelation and Pearson Correlation
limma duplicatecorrelation
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 150
6
votes
4
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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
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4
replies
2.0k
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
3.4k
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
7.5 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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1.8k
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 7.6 years ago by ★ 7.9k • written 7.6 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
993
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
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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 9.4 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
3.4k
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
941
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
692
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
936
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
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1.2k
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Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
8.5 years ago svlachavas ▴ 830
30 results • Page 1 of 1
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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