Showing : variancePartition • reset
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
5 weeks ago GJ • 0
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2
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 weeks ago by 52k • written 11 weeks ago by ▴ 10
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
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511
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
3 months ago • updated 12 weeks ago abadgerw • 0
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5
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746
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
3 months ago • updated 11 weeks ago abadgerw • 0
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9
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949
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Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 5 months ago by 52k • written 5 months ago by • 0
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623
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
10 months ago Le • 0
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4
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1.6k
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BiocParallel serialization errors on Windows
variancePartition BiocParallel
14 months ago hayleyw • 0
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7
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1.4k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 14 months ago by 52k • written 16 months ago by • 0
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9
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
18 months ago hayleyw • 0
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5
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2.3k
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How many parameters should be included in the model design for deseq2?
DESeq2 variancePartition
23 months ago • updated 22 months ago Weiqian ▴ 10
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4
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1.1k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
23 months ago DH • 0
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5
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1.4k
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Semi-technical replicates and voom sample weights
variancePa variancePartition limma-voom dream
updated 24 months ago by 52k • written 24 months ago by • 0
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Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
2.5 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 3.6 years ago by 52k • written 3.6 years ago by • 0
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limma - contrast matrix hypothesis testing
limma variancePartition
updated 3.6 years ago by 52k • written 3.7 years ago by ▴ 30
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What are cov.coefficients and cov.coefficients.list returned by dream()?
variancePartition limma
3.8 years ago Junghoon ▴ 10
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1.4k
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Error while running variancePartition::dream()
variancePartition limma BiocParallel
3.8 years ago Junghoon ▴ 10
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1
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1.4k
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Excessive memory requirement of variancePartition::dream()
BiocParallel limma variancePartition
3.8 years ago • updated 3.7 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 5.4 years ago by 52k • written 5.4 years ago by ▴ 20
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8
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Results from variancePartition not matching those from lme4
variancepartition lme4 mixedmodel
updated 5.4 years ago by ▴ 170 • written 5.5 years ago by • 0
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3
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2.4k
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Blocking factor in limma/voom vs. variancePartition/dream analysis.
limma voom variancePartition dream
updated 5.4 years ago by ▴ 170 • written 5.6 years ago by ▴ 50
22 results • Page 1 of 1
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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