Showing : duplicatecorrelation • reset
2
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Multi-factorial design for patient-replicates from different time points using duplicate correlation LIMMA Voom
limma limma voom duplicatecorrelation
7.2 years ago alva.james • 0
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
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 8.6 years ago by 50k • written 8.6 years ago by ▴ 830
6
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7
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1.8k
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duplicateCorrelation and Pearson Correlation
limma duplicatecorrelation
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 150
8
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7
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4.8k
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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
0
votes
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
1
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7
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3.0k
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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
1
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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 9.6 years ago by ★ 4.0k
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 5.6 years ago by ▴ 90
6
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4
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1.7k
views
Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 30
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 6.7 years ago by 50k • written 6.7 years ago by ▴ 180
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
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 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 80
4
votes
4
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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 ★ 4.0k
3
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4
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1.9k
views
Random effects with limma's camera()
limma camera duplicatecorrelation
updated 8.3 years ago by 50k • written 8.3 years ago by ▴ 30
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
2
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4
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1.0k
views
limma: treating multiple variables as random effects in duplicateCorrelation()
limma duplicateCorrelation
updated 5.1 years ago by 50k • written 5.1 years ago by • 0
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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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
6.9 years ago • updated 6.8 years ago LR0306 ▴ 10
1
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3
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970
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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
5
votes
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
1
vote
2
replies
263
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
9 days ago • updated 8 days ago Dylan.Sheerin • 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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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
0
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2
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703
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Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
3
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2
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1.5k
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Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
2.5 years ago altintas.ali • 0
0
votes
1
reply
953
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
0
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1
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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
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 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
0
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0
replies
1.3k
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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
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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