Showing : duplicatecorrelation • reset
2
votes
9
replies
1.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
updated 8 days ago by 51k • written 19 days ago by • 0
4
votes
6
replies
1.0k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
26 days ago • updated 17 days ago altintas.ali • 0
1
vote
2
replies
579
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
6 months ago Dylan.Sheerin • 0
3
votes
2
replies
1.8k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 19 days ago by 51k • written 3.0 years ago by • 0
1
vote
3
replies
1.2k
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 4.0 years ago by 51k • written 4.0 years ago by • 0
0
votes
1
reply
1.1k
views
Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
8
votes
7
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6.0k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
5
votes
3
replies
1.4k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
0
votes
2
replies
829
views
Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.5 years ago by 67k • written 5.5 years ago by • 0
2
votes
4
replies
1.2k
views
limma: treating multiple variables as random effects in duplicateCorrelation()
limma duplicateCorrelation
updated 5.6 years ago by 51k • written 5.6 years ago by • 0
2
votes
4
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1.5k
views
limma voom - time course experiment - multi level experiment
limma duplicatecorrelation limma voom
6.5 years ago • updated 5.7 years ago SPbeginner • 0
6
votes
4
replies
2.1k
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 30
10
votes
5
replies
2.9k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 6.0 years ago by 51k • written 6.0 years ago by ▴ 100
3
votes
4
replies
2.4k
views
limma-voom WithQualityWeights and duplicateCorrelation in RNA-seq
voomwithqualityweights limma voom duplicatecorrelation
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 80
1
vote
1
reply
1.8k
views
Limma with paired samples and SVA
limma sva duplicatecorrelation estimatecellcounts
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
10
votes
4
replies
2.4k
views
limma-trend with random effects and/or array weights
limma-trend duplicatecorrelation arrayweights limma
updated 7.1 years ago by 51k • written 7.1 years ago by ▴ 180
0
votes
7
replies
2.8k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.3 years ago by ▴ 130 • written 7.3 years ago by ▴ 90
4
votes
3
replies
1.6k
views
Accounting for both categorical and numerical possible confounding variables in the limmaVoom pipeline
limma limma voom duplicatecorrelation
7.3 years ago LR0306 ▴ 10
4
votes
4
replies
2.5k
views
Using duplicateCorrelation to handle replicate samples
limma duplicatecorrelation replicates
7.5 years ago rwalke13 • 0
2
votes
11
replies
2.5k
views
Multi-factorial design for patient-replicates from different time points using duplicate correlation LIMMA Voom
limma limma voom duplicatecorrelation
7.7 years ago alva.james • 0
6
votes
7
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2.0k
views
duplicateCorrelation and Pearson Correlation
limma duplicatecorrelation
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 150
4
votes
2
replies
2.5k
views
Limma, remove batch effects and technical replicates
Limma removebatcheffect() duplicatecorrelation
8.1 years ago John ▴ 10
4
votes
4
replies
3.9k
views
limma - technical replicates: duplicateCorrelation() or avereps()?
limma duplicatecorrelation avereps
updated 8.1 years ago by 51k • written 8.1 years ago by ★ 4.1k
3
votes
3
replies
2.7k
views
Duplicate Correlation with technical replicates
limma duplicatecorrelation
updated 8.2 years ago by ★ 7.9k • written 8.2 years ago by • 0
3
votes
4
replies
2.1k
views
Random effects with limma's camera()
limma camera duplicatecorrelation
updated 8.8 years ago by 51k • written 8.8 years ago by ▴ 30
8
votes
8
replies
4.8k
views
Limma: fit a model with duplicateCorrelation()
limma microarray duplicatecorrelation technical replicates linear model
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 150
2
votes
6
replies
3.0k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma microarray multifactorial design duplicatecorrelation model.matrix
8.9 years ago Konstantinos Yeles ▴ 80
0
votes
1
reply
1.4k
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
8.9 years ago svlachavas ▴ 830
4
votes
8
replies
1.9k
views
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 9.1 years ago by 51k • written 9.1 years ago by ▴ 830
0
votes
0
replies
1.4k
views
Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
9.1 years ago svlachavas ▴ 830
2
votes
2
replies
1.6k
views
Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
limma duplicatecorrelation arrayweights
9.1 years ago willj ▴ 30
1
vote
7
replies
3.3k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 9 months ago by ★ 5.2k • written 10.0 years ago by • 0
1
vote
6
replies
3.7k
views
Limma: advice needed for best approach for joint paired and unpaired analyses in unbalanced intervention study
limma paired unpaired duplicateCorrelation
updated 10.0 years ago by ▴ 10 • written 10.0 years ago by ★ 4.1k
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Comment: Bioconductor 3.18 is Released! by thelmatertl • 0
This is a release that expresses gratitude to the developers and community members for their contributions and the new features enhance the…
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by daniela.gutierrezandrade • 0
Hello, I am running into a similar issue. After setting the design, at the beginning of the analysis I filter rows with low counts. d…
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0
Thank you so much for all of your help! I really appreciate it!
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by Gordon Smyth 51k
Thanks for extra info, but be careful that the Bioconductor support site requires code to be an markdown format. Copying code with prompts …
Comment: Limma- Print-tip loess normalisation-printer layout information does not match M by dseauer • 0
Thank you so much for your reply! I am sincerely sorry- of course I do not have multiple GAL files- just one- I meant gpr files! I am so so…
Votes
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
biomaRt rnorvegicus_gene_ensembl not available anymore
A: Does edgeR need to specify reference group?
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