Showing : variancepartition • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 8 days ago by 53k • written 13 days 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
9 months ago GJ • 0
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2
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848
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 months ago by 53k • written 10 months ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 10 months ago by 68k • written 10 months ago by • 0
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
11 months ago • updated 10 months ago abadgerw • 0
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
11 months ago • updated 10 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 13 months ago by 53k • written 13 months ago by • 0
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
18 months ago Le • 0
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2.3k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
22 months ago hayleyw • 0
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 22 months ago by 53k • written 2.0 years ago by • 0
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
2.1 years ago hayleyw • 0
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2.8k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
2.5 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
2.6 years ago DH • 0
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5
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1.8k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.2 years ago Jonathan • 0
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Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 4.2 years ago by 53k • written 4.2 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 4.3 years ago by 53k • written 4.3 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
4.5 years ago Junghoon ▴ 10
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1.7k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
4.5 years ago Junghoon ▴ 10
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
4.5 years ago • updated 4.3 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 6.0 years ago by 53k • written 6.0 years ago by ▴ 20
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 6.0 years ago by ▴ 170 • written 6.1 years ago by • 0
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3
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2.9k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 6.0 years ago by ▴ 170 • written 6.3 years ago by ▴ 50
23 results • Page 1 of 1
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Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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