Showing : duplicateCorrelation • reset
8
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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
8
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8
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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
4
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4
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3.5k
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limma - technical replicates: duplicateCorrelation() or avereps()?
limma duplicatecorrelation avereps
updated 7.6 years ago by 50k • written 7.6 years ago by ★ 3.9k
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6
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3.5k
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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
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7
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2.9k
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Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
2
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6
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2.8k
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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
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
0
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7
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2.5k
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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
3
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3
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2.5k
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Duplicate Correlation with technical replicates
limma duplicatecorrelation
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by • 0
4
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2
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2.3k
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Limma, remove batch effects and technical replicates
Limma removebatcheffect() duplicatecorrelation
7.6 years ago John ▴ 10
2
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11
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2.2k
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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
10
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4
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2.1k
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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
3
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4
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2.1k
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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
4
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4
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2.1k
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Using duplicateCorrelation to handle replicate samples
limma duplicatecorrelation replicates
7.0 years ago rwalke13 • 0
3
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4
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1.9k
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Random effects with limma's camera()
limma camera duplicatecorrelation
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 30
6
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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 7.6 years ago by ▴ 150
4
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8
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1.7k
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Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 8.6 years ago by 50k • written 8.6 years ago by ▴ 830
6
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4
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1.7k
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Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
1
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1
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1.6k
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Limma with paired samples and SVA
limma sva duplicatecorrelation estimatecellcounts
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
3
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2
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Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
2.4 years ago altintas.ali • 0
2
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2
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1.5k
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Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
limma duplicatecorrelation arrayweights
8.6 years ago willj ▴ 30
4
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3
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1.4k
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Accounting for both categorical and numerical possible confounding variables in the limmaVoom pipeline
limma limma voom duplicatecorrelation
6.8 years ago LR0306 ▴ 10
2
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4
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1.3k
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limma voom - time course experiment - multi level experiment
limma duplicatecorrelation limma voom
6.0 years ago • updated 5.2 years ago SPbeginner • 0
0
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1
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1.3k
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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
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0
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Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
8.6 years ago svlachavas ▴ 830
5
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3
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1.2k
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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
2
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4
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999
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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
1
vote
3
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955
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Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.5 years ago by 50k • written 3.5 years ago by • 0
0
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1
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946
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Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by • 0
0
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2
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698
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Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
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