Showing : variancePartition • reset
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
7 days ago GJ • 0
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483
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 6 weeks ago by 52k • written 6 weeks ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
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471
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 7 weeks ago abadgerw • 0
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5
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683
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 7 weeks ago abadgerw • 0
2
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9
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886
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 4 months ago by 52k • written 4 months ago by • 0
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586
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 months ago Le • 0
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4
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1.5k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
13 months ago hayleyw • 0
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7
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1.3k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 13 months ago by 52k • written 15 months ago by • 0
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9
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1.4k
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
17 months ago hayleyw • 0
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2.2k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
22 months ago • updated 21 months ago Weiqian ▴ 10
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1.0k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
22 months ago DH • 0
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5
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1.4k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 22 months ago by 52k • written 23 months ago by • 0
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619
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.4 years ago Jonathan • 0
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 3.5 years ago by 52k • written 3.5 years ago by • 0
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1.6k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.6 years ago by 52k • written 3.6 years ago by ▴ 30
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1.0k
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
3.7 years ago Junghoon ▴ 10
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1.4k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
3.7 years ago Junghoon ▴ 10
0
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1
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1.3k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
3.7 years ago • updated 3.6 years ago Junghoon ▴ 10
9
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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 5.3 years ago by 52k • written 5.3 years ago by ▴ 20
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8
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.3 years ago by ▴ 170 • written 5.4 years ago by • 0
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3
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2.4k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.3 years ago by ▴ 170 • written 5.6 years ago by ▴ 50
22 results • Page 1 of 1
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Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Answer: EdgeR Biological CVs by Gordon Smyth 52k
I think your questions are answered by the published paper. You might also like to consult recent papers on edgeR by Yunshun Chen and Pedro…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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