Showing : variancepartition • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 10 weeks ago by 53k • written 11 weeks ago by • 0
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
11 months ago GJ • 0
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2
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944
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 months ago by 53k • written 12 months ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 12 months ago by 68k • written 12 months ago by • 0
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
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1.2k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
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9
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1.6k
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 15 months ago by 53k • written 15 months ago by • 0
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984
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
20 months ago Le • 0
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4
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2.4k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
2.0 years ago hayleyw • 0
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1.8k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.0 years ago by 53k • written 2.2 years ago by • 0
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
2.3 years ago hayleyw • 0
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5
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2.9k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.7 years ago • updated 2.6 years ago Weiqian ▴ 10
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1.3k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.8 years ago DH • 0
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5
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1.9k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
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884
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.3 years ago Jonathan • 0
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1.9k
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
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3
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1.9k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 4.5 years ago by 53k • written 4.5 years ago by ▴ 30
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1.2k
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
4.6 years ago Junghoon ▴ 10
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1.7k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
4.6 years ago Junghoon ▴ 10
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1.6k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
4.6 years ago • updated 4.5 years ago Junghoon ▴ 10
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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 6.2 years ago by 53k • written 6.2 years ago by ▴ 20
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 6.2 years ago by ▴ 170 • written 6.3 years ago by • 0
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3
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3.0k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 6.2 years ago by ▴ 170 • written 6.5 years ago by ▴ 50
23 results • Page 1 of 1
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Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. There is no need to form "reduced models…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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