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Showing :
variancepartition
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0
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150
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makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
10 days ago • updated 4 days ago
abadgerw
• 0
0
votes
1
reply
259
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
10 days ago • updated 4 days ago
abadgerw
• 0
2
votes
9
replies
779
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR
variancePartition
updated 11 weeks ago by
Gordon Smyth
51k • written 12 weeks ago by
Seymoo
• 0
1
vote
2
replies
517
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
7 months ago
Le
• 0
1
vote
4
replies
1.3k
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
11 months ago
hayleyw
• 0
1
vote
7
replies
1.2k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 11 months ago by
Gordon Smyth
51k • written 13 months ago by
Gimena
• 0
0
votes
9
replies
1.3k
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
15 months ago
hayleyw
• 0
1
vote
5
replies
2.0k
views
How many parameters should be included in the model design for deseq2?
DESeq2
variancePartition
20 months ago • updated 19 months ago
Weiqian
▴ 10
1
vote
4
replies
959
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq
variancePartition
edgeR
dream
20 months ago
DH
• 0
0
votes
5
replies
1.3k
views
Semi-technical replicates and voom sample weights
variancePa
variancePartition
limma-voom
dream
updated 20 months ago by
Gordon Smyth
51k • written 20 months ago by
Le
• 0
0
votes
0
replies
586
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
2.3 years ago
Jonathan
• 0
1
vote
1
reply
1.5k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR
limma
variancePartition
updated 3.3 years ago by
Gordon Smyth
51k • written 3.3 years ago by
jackgisby
• 0
1
vote
3
replies
1.5k
views
limma - contrast matrix hypothesis testing
limma
variancePartition
updated 3.4 years ago by
Gordon Smyth
51k • written 3.4 years ago by
jarod
▴ 30
1
vote
0
replies
978
views
What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition
limma
3.6 years ago
Junghoon
▴ 10
0
votes
1
reply
1.3k
views
Error while running variancePartition::dream()
variancePartition
limma
BiocParallel
3.6 years ago
Junghoon
▴ 10
0
votes
1
reply
1.3k
views
Excessive memory requirement of variancePartition::dream()
BiocParallel
limma
variancePartition
3.6 years ago • updated 3.4 years ago
Junghoon
▴ 10
9
votes
11
replies
2.9k
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 5.1 years ago by
Gordon Smyth
51k • written 5.1 years ago by
hermidalc
▴ 20
3
votes
8
replies
1.9k
views
Results from variancePartition not matching those from lme4
variancepartition
lme4
mixedmodel
updated 5.1 years ago by
gabriel.hoffman
▴ 160 • written 5.2 years ago by
c.taylor
• 0
4
votes
3
replies
2.2k
views
Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma
voom
variancePartition
dream
updated 5.1 years ago by
gabriel.hoffman
▴ 160 • written 5.4 years ago by
Ben
▴ 50
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Answer: UniProt.ws query loading indefinitely
by
James W. MacDonald
67k
It should be almost instantaneous. Do you have internet access on the local computer? ``` > system.time(up <- UniProt.ws()) user s…
Comment: Package needs internet access
by
James W. MacDonald
67k
I am not sure what you mean by 'only used to create that genome file'. What's happening is you are converting the `seqlevels` of an existin…
Comment: Identifying potentially associated gene set to drug response using GSVA
by
wtao7767
• 0
https://sprunki.net/ Incredibox Sprunki is a creative mod of the classic Incredibox game, blending Sprunki's unique style with interactive …
Answer: Allele frequencies for ALL alleles of one SNP ?
by
Abiologist
• 0
I've discovered that rsnps::ncbi_snp_query(snp_id) does actually give this information - at the bottom of the result$maf_population table. …
Answer: Identifying potentially associated gene set to drug response using GSVA
by
Robert Castelo
★ 3.4k
Hi, if you want to do some formal inference about the effect of a drug at RNA level, then I would recommend you doing a differential expres…
Votes
Answer: Package needs internet access
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
Comment: Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
Dotplot from enricher outputting very few genes
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James W. MacDonald
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shepherl
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Robert Castelo
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Ahdee
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