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variancepartition
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182
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
10 weeks ago
GJ
• 0
0
votes
2
replies
576
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
Lina
▴ 10
0
votes
9
replies
1.1k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
abadgerw
• 0
1
vote
3
replies
557
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
4 months ago • updated 3 months ago
abadgerw
• 0
0
votes
5
replies
816
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
4 months ago • updated 3 months ago
abadgerw
• 0
2
votes
9
replies
1.0k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR
variancePartition
updated 6 months ago by
Gordon Smyth
52k • written 7 months ago by
Seymoo
• 0
1
vote
2
replies
680
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
11 months ago
Le
• 0
1
vote
4
replies
1.8k
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
15 months ago
hayleyw
• 0
1
vote
7
replies
1.4k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 15 months ago by
Gordon Smyth
52k • written 17 months ago by
Gimena
• 0
0
votes
9
replies
1.5k
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
19 months ago
hayleyw
• 0
1
vote
5
replies
2.5k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
24 months ago • updated 23 months ago
Weiqian
▴ 10
1
vote
4
replies
1.1k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
2.0 years ago
DH
• 0
0
votes
5
replies
1.5k
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Le
• 0
0
votes
0
replies
669
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
2.6 years ago
Jonathan
• 0
1
vote
1
reply
1.7k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR
limma
variancePartition
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
jackgisby
• 0
1
vote
3
replies
1.6k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 3.7 years ago by
Gordon Smyth
52k • written 3.8 years ago by
jarod
▴ 30
1
vote
0
replies
1.1k
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition
limma
3.9 years ago
Junghoon
▴ 10
0
votes
1
reply
1.4k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.9 years ago
Junghoon
▴ 10
0
votes
1
reply
1.4k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.9 years ago • updated 3.8 years ago
Junghoon
▴ 10
9
votes
11
replies
3.2k
views
dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream
variancePartition
limma
differential expression
repeated measures
updated 5.5 years ago by
Gordon Smyth
52k • written 5.5 years ago by
hermidalc
▴ 20
3
votes
8
replies
2.2k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 5.5 years ago by
gabriel.hoffman
▴ 170 • written 5.6 years ago by
c.taylor
• 0
4
votes
3
replies
2.5k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 5.5 years ago by
gabriel.hoffman
▴ 170 • written 5.7 years ago by
Ben
▴ 50
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Comment: Annotation package for Manduca sexta
by
GA
▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder
by
ATpoint
★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species
by
Mike Smith
★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
by
Gordon Smyth
52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas
by
James W. MacDonald
68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
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