Showing : duplicateCorrelation • reset
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
5 weeks ago Dylan.Sheerin • 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
2.6 years ago altintas.ali • 0
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3
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Limma: Differential expression with two batch effects , location and batch.
duplicatecorrelation BatchEffect limma corfit
updated 3.6 years ago by 51k • written 3.6 years ago by • 0
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979
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Limma: Correct for location and batch effect
limma BatchEffect duplicatecorrelation block batch
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
8
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7
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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 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 50
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 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
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2
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716
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Use of limma for multi-level experiments
limma duplicateCorrelation
updated 5.1 years ago by 66k • written 5.1 years ago by • 0
2
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4
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1.0k
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limma: treating multiple variables as random effects in duplicateCorrelation()
limma duplicateCorrelation
updated 5.2 years ago by 51k • written 5.2 years ago by • 0
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4
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1.4k
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limma voom - time course experiment - multi level experiment
limma duplicatecorrelation limma voom
6.1 years ago • updated 5.3 years ago SPbeginner • 0
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4
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1.8k
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Limma Voom duplicateCorrelation Design
limma voom duplicatecorrelation
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 30
10
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5
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2.6k
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limma-voom duplicateCorrelation once or twice, difference?
limma-voom duplicatecorrelation random effects
updated 5.6 years ago by 51k • written 5.6 years ago by ▴ 90
3
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4
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2.2k
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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
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1
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1.7k
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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
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4
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limma-trend with random effects and/or array weights
limma-trend duplicatecorrelation arrayweights limma
updated 6.7 years ago by 51k • written 6.7 years ago by ▴ 180
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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 6.9 years ago by ▴ 130 • written 6.9 years ago by ▴ 90
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
6.9 years ago LR0306 ▴ 10
4
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4
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2.2k
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Using duplicateCorrelation to handle replicate samples
limma duplicatecorrelation replicates
7.1 years ago rwalke13 • 0
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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
7.2 years ago alva.james • 0
6
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7
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1.8k
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duplicateCorrelation and Pearson Correlation
limma duplicatecorrelation
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 150
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
7.7 years ago John ▴ 10
4
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4
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3.6k
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limma - technical replicates: duplicateCorrelation() or avereps()?
limma duplicatecorrelation avereps
updated 7.7 years ago by 51k • written 7.7 years ago by ★ 4.0k
3
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3
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2.5k
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Duplicate Correlation with technical replicates
limma duplicatecorrelation
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by • 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 8.3 years ago by 51k • written 8.3 years ago by ▴ 30
8
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8
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4.5k
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Limma: fit a model with duplicateCorrelation()
limma microarray duplicatecorrelation technical replicates linear model
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 150
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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
8.5 years ago Konstantinos Yeles ▴ 80
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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
8.5 years ago svlachavas ▴ 830
4
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8
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1.8k
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Combination of duplicateCorrelation with arrayWeights to increase power for DE detection in multilevel experiments
limma duplicatecorrelation arrayweights microarray
updated 8.7 years ago by 51k • written 8.7 years ago by ▴ 830
0
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0
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1.3k
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Possible methodologies for constructing multi-level comparisons in limma
limma paired analysis multiple factor design affymetrix microarrays duplicatecorrelation
8.7 years ago svlachavas ▴ 830
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
8.7 years ago willj ▴ 30
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7
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3.0k
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Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 4 months ago by ★ 5.2k • written 9.6 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 9.6 years ago by ▴ 10 • written 9.6 years ago by ★ 4.0k
31 results • Page 1 of 1
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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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