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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
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434
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
13 months ago GJ • 0
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2
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1.0k
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 months ago by 53k • written 14 months ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 14 months ago by 68k • written 14 months ago by • 0
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1.0k
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
15 months ago • updated 14 months ago abadgerw • 0
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5
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1.3k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
15 months ago • updated 14 months ago abadgerw • 0
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 17 months ago by 53k • written 17 months ago by • 0
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1.1k
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
22 months ago Le • 0
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4
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2.7k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
2.2 years ago hayleyw • 0
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1.9k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.2 years ago by 53k • written 2.3 years ago by • 0
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
2.5 years ago hayleyw • 0
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5
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3.1k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.9 years ago • updated 2.8 years ago Weiqian ▴ 10
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4
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1.5k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.9 years ago DH • 0
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5
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2.0k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.9 years ago by 53k • written 3.0 years ago by • 0
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958
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.5 years ago Jonathan • 0
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2.0k
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 4.6 years ago by 53k • written 4.6 years ago by • 0
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3
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2.0k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 30
1
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0
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1.4k
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
4.8 years ago Junghoon ▴ 10
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1.8k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
4.8 years ago Junghoon ▴ 10
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1
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1.7k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
4.8 years ago • updated 4.6 years ago Junghoon ▴ 10
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4.0k
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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 6.3 years ago by 53k • written 6.4 years ago by ▴ 20
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8
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2.8k
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 6.4 years ago by ▴ 170 • written 6.5 years ago by • 0
4
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3
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3.4k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 6.4 years ago by ▴ 170 • written 6.6 years ago by ▴ 50
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Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
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Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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