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variancepartition
•
reset
1
vote
2
replies
246
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago
Le
• 0
1
vote
4
replies
694
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
5 months ago
hayleyw
• 0
1
vote
7
replies
889
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 5 months ago by
Gordon Smyth
50k • written 7 months ago by
Gimena
• 0
0
votes
9
replies
879
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
9 months ago
hayleyw
• 0
1
vote
5
replies
1.6k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
14 months ago • updated 13 months ago
Weiqian
▴ 10
1
vote
4
replies
724
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
14 months ago
DH
• 0
0
votes
5
replies
992
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Le
• 0
0
votes
0
replies
462
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
21 months ago
Jonathan
• 0
1
vote
1
reply
1.3k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR
limma
variancePartition
updated 2.8 years ago by
Gordon Smyth
50k • written 2.8 years ago by
jackgisby
• 0
1
vote
3
replies
1.3k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 2.9 years ago by
Gordon Smyth
50k • written 2.9 years ago by
jarod
▴ 30
1
vote
0
replies
817
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition
limma
3.1 years ago
Junghoon
▴ 10
0
votes
1
reply
1.2k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.1 years ago
Junghoon
▴ 10
0
votes
1
reply
1.1k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.1 years ago • updated 2.9 years ago
Junghoon
▴ 10
8
votes
11
replies
2.4k
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 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
hermidalc
▴ 20
3
votes
8
replies
1.5k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 4.6 years ago by
gabriel.hoffman
▴ 110 • written 4.7 years ago by
c.taylor
• 0
4
votes
3
replies
1.7k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 4.6 years ago by
gabriel.hoffman
▴ 110 • written 4.9 years ago by
Ben
▴ 50
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Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
James W. MacDonald
66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf
by
Brandon
• 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet
by
Kelly Street
• 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet
by
Michael Love
42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM
by
Vitor
• 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). !…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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