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variancePartition
•
reset
0
votes
0
replies
3
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
10 minutes ago
Le
• 0
1
vote
4
replies
533
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
4 months ago
hayleyw
• 0
1
vote
7
replies
791
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
803
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
7 months ago
hayleyw
• 0
1
vote
5
replies
1.4k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
12 months ago • updated 11 months ago
Weiqian
▴ 10
1
vote
4
replies
664
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
919
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Le
• 0
0
votes
0
replies
435
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 2.7 years ago by
Gordon Smyth
50k • written 2.7 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
772
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 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
hermidalc
▴ 20
3
votes
8
replies
1.5k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 4.5 years ago by
gabriel.hoffman
▴ 100 • written 4.6 years ago by
c.taylor
• 0
4
votes
3
replies
1.6k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 4.5 years ago by
gabriel.hoffman
▴ 100 • written 4.8 years ago by
Ben
▴ 50
16 results • Page
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Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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