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variancepartition
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207
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
3 months ago
GJ
• 0
0
votes
2
replies
619
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 4 months ago by
Gordon Smyth
52k • written 4 months ago by
Lina
▴ 10
0
votes
9
replies
1.2k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
abadgerw
• 0
1
vote
3
replies
598
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
5 months ago
abadgerw
• 0
0
votes
5
replies
889
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
5 months ago • updated 4 months ago
abadgerw
• 0
2
votes
9
replies
1.1k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR
variancePartition
updated 8 months ago by
Gordon Smyth
52k • written 8 months ago by
Seymoo
• 0
1
vote
2
replies
731
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
12 months ago
Le
• 0
1
vote
4
replies
1.9k
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
16 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 16 months ago by
Gordon Smyth
52k • written 18 months ago by
Gimena
• 0
0
votes
9
replies
1.6k
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
20 months ago
hayleyw
• 0
1
vote
5
replies
2.6k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
2.1 years ago • updated 2.0 years 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
2.1 years ago
DH
• 0
0
votes
5
replies
1.5k
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 2.2 years ago by
Gordon Smyth
52k • written 2.2 years ago by
Le
• 0
0
votes
0
replies
688
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
2.7 years ago
Jonathan
• 0
1
vote
1
reply
1.7k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR
limma
variancePartition
updated 3.8 years ago by
Gordon Smyth
52k • written 3.8 years ago by
jackgisby
• 0
1
vote
3
replies
1.7k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 3.8 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
4.0 years ago
Junghoon
▴ 10
0
votes
1
reply
1.5k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
4.0 years ago
Junghoon
▴ 10
0
votes
1
reply
1.4k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
4.0 years ago • updated 3.9 years ago
Junghoon
▴ 10
9
votes
11
replies
3.3k
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 5.6 years ago by
Gordon Smyth
52k • written 5.6 years ago by
hermidalc
▴ 20
3
votes
8
replies
2.2k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 5.6 years ago by
gabriel.hoffman
▴ 170 • written 5.7 years ago by
c.taylor
• 0
4
votes
3
replies
2.7k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 5.6 years ago by
gabriel.hoffman
▴ 170 • written 5.8 years ago by
Ben
▴ 50
22 results • Page
1 of 1
Recent ...
Replies
Comment: Intepretation of results
by
Tom
• 0
[Locksmith Wombwell][1] I have been interested in using AUCell as a way to determine significantly enriched pathways in my single cell spat…
Comment: Gene Ontology (GO) Analysis
by
Tom
• 0
[Locksmith near me][1] Hello, I'm learning about Gene Ontology analysis. I'm trying to understand the difference between the hyperGTest fun…
Comment: DiffBind; Error: No sites have activity greater than filter value
by
etiennedanis
• 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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