Showing : duplicatecorrelation • reset
10
votes
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
4
votes
2
replies
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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4
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1.3k
views
limma voom - time course experiment - multi level experiment
limma duplicatecorrelation limma voom
6.0 years ago • updated 5.2 years ago SPbeginner • 0
1
vote
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
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
8
votes
7
replies
4.8k
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
4
votes
8
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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 8.6 years ago by ▴ 830
4
votes
3
replies
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
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
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
0
votes
7
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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
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
3
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4
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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
6
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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
2
votes
4
replies
998
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
0
votes
2
replies
697
views
Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
3
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2
replies
1.5k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
2.4 years ago altintas.ali • 0
1
vote
7
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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
2
votes
2
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1.5k
views
Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
limma duplicatecorrelation arrayweights
8.6 years ago willj ▴ 30
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
3
votes
4
replies
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
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
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
2
votes
11
replies
2.2k
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
0
votes
0
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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
0
votes
1
reply
945
views
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
1
vote
3
replies
954
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.4 years ago by 50k • written 3.5 years ago by • 0
0
votes
1
reply
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
30 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
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…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea() by James W. MacDonald 65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
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Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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