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variancePartition
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317
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
7 months ago
GJ
• 0
0
votes
2
replies
793
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 8 months ago by
Gordon Smyth
52k • written 9 months ago by
Lina
▴ 10
0
votes
9
replies
1.5k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
abadgerw
• 0
1
vote
3
replies
756
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
9 months ago
abadgerw
• 0
0
votes
5
replies
1.1k
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
9 months ago
abadgerw
• 0
2
votes
9
replies
1.3k
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR
variancePartition
updated 12 months ago by
Gordon Smyth
52k • written 12 months ago by
Seymoo
• 0
1
vote
2
replies
866
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
16 months ago
Le
• 0
1
vote
4
replies
2.2k
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
20 months ago
hayleyw
• 0
1
vote
7
replies
1.7k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 21 months ago by
Gordon Smyth
52k • written 23 months ago by
Gimena
• 0
0
votes
9
replies
1.8k
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
2.0 years ago
hayleyw
• 0
1
vote
5
replies
2.7k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
2.4 years ago
Weiqian
▴ 10
1
vote
4
replies
1.3k
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
2.5 years ago
DH
• 0
0
votes
5
replies
1.7k
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 2.5 years ago by
Gordon Smyth
52k • written 2.5 years ago by
Le
• 0
0
votes
0
replies
769
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
3.1 years ago
Jonathan
• 0
1
vote
1
reply
1.8k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR
limma
variancePartition
updated 4.1 years ago by
Gordon Smyth
52k • written 4.1 years ago by
jackgisby
• 0
1
vote
3
replies
1.8k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 4.2 years ago by
Gordon Smyth
52k • written 4.2 years ago by
jarod
▴ 30
1
vote
0
replies
1.2k
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition
limma
4.3 years ago
Junghoon
▴ 10
0
votes
1
reply
1.6k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
4.4 years ago • updated 4.3 years ago
Junghoon
▴ 10
0
votes
1
reply
1.5k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
4.3 years ago • updated 4.2 years ago
Junghoon
▴ 10
10
votes
11
replies
3.5k
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 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
hermidalc
▴ 20
3
votes
8
replies
2.4k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 5.9 years ago by
gabriel.hoffman
▴ 170 • written 6.0 years ago by
c.taylor
• 0
4
votes
3
replies
2.9k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 5.9 years ago by
gabriel.hoffman
▴ 170 • written 6.2 years ago by
Ben
▴ 50
22 results • Page
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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