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variancepartition
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128
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
19 days ago
GJ
• 0
0
votes
2
replies
498
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 8 weeks ago by
Gordon Smyth
52k • written 8 weeks ago by
Lina
▴ 10
0
votes
9
replies
967
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 8 weeks ago by
James W. MacDonald
67k • written 9 weeks ago by
abadgerw
• 0
1
vote
3
replies
489
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
12 weeks ago • updated 9 weeks ago
abadgerw
• 0
0
votes
5
replies
716
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
12 weeks ago • updated 8 weeks ago
abadgerw
• 0
2
votes
9
replies
916
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR
variancePartition
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
Seymoo
• 0
1
vote
2
replies
602
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 months ago
Le
• 0
1
vote
4
replies
1.5k
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
13 months ago
hayleyw
• 0
1
vote
7
replies
1.3k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 14 months ago by
Gordon Smyth
52k • written 16 months ago by
Gimena
• 0
0
votes
9
replies
1.4k
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
17 months ago
hayleyw
• 0
1
vote
5
replies
2.2k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
22 months ago • updated 21 months ago
Weiqian
▴ 10
1
vote
4
replies
1.0k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
23 months ago
DH
• 0
0
votes
5
replies
1.4k
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 23 months ago by
Gordon Smyth
52k • written 23 months ago by
Le
• 0
0
votes
0
replies
632
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
2.5 years ago
Jonathan
• 0
1
vote
1
reply
1.6k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR
limma
variancePartition
updated 3.5 years ago by
Gordon Smyth
52k • written 3.5 years ago by
jackgisby
• 0
1
vote
3
replies
1.6k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 3.6 years ago by
Gordon Smyth
52k • written 3.6 years ago by
jarod
▴ 30
1
vote
0
replies
1.0k
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition
limma
3.8 years ago
Junghoon
▴ 10
0
votes
1
reply
1.4k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.8 years ago
Junghoon
▴ 10
0
votes
1
reply
1.3k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.8 years ago • updated 3.6 years ago
Junghoon
▴ 10
9
votes
11
replies
3.1k
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 5.3 years ago by
Gordon Smyth
52k • written 5.3 years ago by
hermidalc
▴ 20
3
votes
8
replies
2.0k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 5.3 years ago by
gabriel.hoffman
▴ 170 • written 5.4 years ago by
c.taylor
• 0
4
votes
3
replies
2.4k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 5.3 years ago by
gabriel.hoffman
▴ 170 • written 5.6 years ago by
Ben
▴ 50
22 results • Page
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Comment: Unused arguments error without used arguments in GSVA?
by
1sunmic2
• 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA?
by
Axel Klenk
★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions
by
Aaron Lun
★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA
by
User3088
• 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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