Showing : variancePartition • reset
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 23 days ago by 52k • written 24 days ago by ▴ 10
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9
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840
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 25 days ago by 67k • written 4 weeks ago by • 0
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3
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439
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
7 weeks ago • updated 4 weeks ago abadgerw • 0
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5
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643
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
7 weeks ago • updated 28 days ago abadgerw • 0
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9
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858
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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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560
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
8 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
12 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 14 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
16 months ago hayleyw • 0
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5
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2.1k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
21 months ago • updated 20 months ago Weiqian ▴ 10
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4
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994
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
21 months ago DH • 0
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5
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1.3k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 22 months ago by 52k • written 22 months ago by • 0
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609
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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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1.6k
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 3.4 years ago by 52k • written 3.4 years ago by • 0
1
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3
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1.6k
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.5 years ago by 52k • written 3.5 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
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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 3.5 years ago Junghoon ▴ 10
9
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11
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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 5.2 years ago by 52k • written 5.2 years ago by ▴ 20
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.2 years ago by ▴ 170 • written 5.3 years ago by • 0
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3
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2.3k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.2 years ago by ▴ 170 • written 5.5 years ago by ▴ 50
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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
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EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
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