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Showing :
variancePartition
•
reset
1
vote
2
replies
188
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
8 days ago
Le
• 0
1
vote
4
replies
570
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
4 months ago
hayleyw
• 0
1
vote
7
replies
817
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 4 months ago by
Gordon Smyth
50k • written 6 months ago by
Gimena
• 0
0
votes
9
replies
821
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
8 months ago
hayleyw
• 0
1
vote
5
replies
1.5k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
13 months ago • updated 12 months ago
Weiqian
▴ 10
1
vote
4
replies
675
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
13 months ago
DH
• 0
0
votes
5
replies
942
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
446
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
20 months ago
Jonathan
• 0
1
vote
1
reply
1.2k
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
1.2k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 2.8 years ago by
Gordon Smyth
50k • written 2.8 years ago by
jarod
▴ 30
1
vote
0
replies
782
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition
limma
3.0 years ago
Junghoon
▴ 10
0
votes
1
reply
1.1k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.0 years ago
Junghoon
▴ 10
0
votes
1
reply
1.1k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.0 years ago • updated 2.8 years ago
Junghoon
▴ 10
8
votes
11
replies
2.3k
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 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 4.8 years ago by
Ben
▴ 50
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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