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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
3 months ago GJ • 0
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 4 months ago by • 0
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 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 7 months ago by 52k • written 8 months ago by • 0
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
12 months ago Le • 0
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
16 months ago hayleyw • 0
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 16 months ago by 52k • written 18 months ago by • 0
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
20 months ago hayleyw • 0
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.1 years ago • updated 24 months ago Weiqian ▴ 10
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
2.1 years ago DH • 0
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1.5k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.1 years ago by 52k • written 2.2 years ago by • 0
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.7 years ago Jonathan • 0
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 3.8 years ago by 52k • written 3.8 years ago by • 0
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.8 years ago by 52k • written 3.8 years ago by ▴ 30
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
4.0 years ago Junghoon ▴ 10
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1.5k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
4.0 years ago Junghoon ▴ 10
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1.4k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
4.0 years ago • updated 3.8 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 5.5 years ago by 52k • written 5.5 years ago by ▴ 20
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.6 years ago by ▴ 170 • written 5.7 years ago by • 0
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.6 years ago by ▴ 170 • written 5.8 years ago by ▴ 50
22 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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Answer: ROAST for small sets
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