Showing : duplicatecorrelation • reset
2
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12
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1.6k
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limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
8 weeks ago • updated 29 days ago john • 0
4
votes
6
replies
1.1k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
9 weeks ago • updated 8 weeks ago altintas.ali • 0
1
vote
2
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645
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
7 months ago Dylan.Sheerin • 0
3
votes
2
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1.9k
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Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 8 weeks ago by 52k • written 3.1 years ago by • 0
1
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3
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1.2k
views
Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 4.1 years ago by 52k • written 4.1 years ago by • 0
0
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1
reply
1.2k
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Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
8
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7
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6.3k
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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 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
5
votes
3
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1.4k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
0
votes
2
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846
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Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
2
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4
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1.2k
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limma: treating multiple variables as random effects in duplicateCorrelation()
limma duplicateCorrelation
updated 5.7 years ago by 52k • written 5.7 years ago by • 0
2
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4
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1.6k
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limma voom - time course experiment - multi level experiment
limma duplicatecorrelation limma voom
6.6 years ago • updated 5.8 years ago SPbeginner • 0
6
votes
4
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2.1k
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 30
10
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5
replies
2.9k
views
limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 6.1 years ago by 52k • written 6.1 years ago by ▴ 100
3
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4
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2.5k
views
limma-voom WithQualityWeights and duplicateCorrelation in RNA-seq
voomwithqualityweights limma voom duplicatecorrelation
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 80
1
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1
reply
1.9k
views
Limma with paired samples and SVA
limma sva duplicatecorrelation estimatecellcounts
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
10
votes
4
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2.4k
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limma-trend with random effects and/or array weights
limma-trend duplicatecorrelation arrayweights limma
updated 7.2 years ago by 52k • written 7.2 years ago by ▴ 180
0
votes
7
replies
2.8k
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Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 90
4
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3
replies
1.6k
views
Accounting for both categorical and numerical possible confounding variables in the limmaVoom pipeline
limma limma voom duplicatecorrelation
7.5 years ago • updated 7.4 years ago LR0306 ▴ 10
4
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4
replies
2.6k
views
Using duplicateCorrelation to handle replicate samples
limma duplicatecorrelation replicates
7.6 years ago rwalke13 • 0
2
votes
11
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2.5k
views
Multi-factorial design for patient-replicates from different time points using duplicate correlation LIMMA Voom
limma limma voom duplicatecorrelation
7.8 years ago alva.james • 0
6
votes
7
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2.1k
views
duplicateCorrelation and Pearson Correlation
limma duplicatecorrelation
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 150
4
votes
2
replies
2.6k
views
Limma, remove batch effects and technical replicates
Limma removebatcheffect() duplicatecorrelation
8.2 years ago John ▴ 10
4
votes
4
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3.9k
views
limma - technical replicates: duplicateCorrelation() or avereps()?
limma duplicatecorrelation avereps
updated 8.2 years ago by 52k • written 8.2 years ago by ★ 4.1k
3
votes
3
replies
2.8k
views
Duplicate Correlation with technical replicates
limma duplicatecorrelation
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by • 0
3
votes
4
replies
2.2k
views
Random effects with limma's camera()
limma camera duplicatecorrelation
updated 8.9 years ago by 52k • written 8.9 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 8.9 years ago by ★ 28k • written 8.9 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
9.0 years ago Konstantinos Yeles ▴ 80
0
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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
9.0 years ago svlachavas ▴ 840
4
votes
8
replies
2.0k
views
Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 9.2 years ago by 52k • written 9.2 years ago by ▴ 840
0
votes
0
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1.4k
views
Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
9.2 years ago svlachavas ▴ 840
2
votes
2
replies
1.6k
views
Correct use of arrayWeights alongside duplicateCorrelation for microarrays in Limma?
limma duplicatecorrelation arrayweights
9.2 years ago willj ▴ 30
1
vote
7
replies
3.3k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 11 months ago by ★ 5.2k • written 10.1 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 10.1 years ago by ▴ 10 • written 10.2 years ago by ★ 4.1k
33 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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