Bioconductor Model

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429

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DESeq2 LRT Model

updated 14 months ago by Michael Love 40k • written 14 months ago by JaneDoe • 0

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replies

524

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model BatchEffect hidden Design DESeq2

19 months ago m.glymenaki • 0

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767

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DESeq2 ErrorincheckFullRank(modelMatrix) model

updated 2.5 years ago by Michael Love 40k • written 2.5 years ago by Isabelle • 0

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replies

693

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diffbind blocking model

updated 2.6 years ago by Rory Stark ★ 4.8k • written 3.6 years ago by melnuesch ▴ 10

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646

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deseq2 interaction model

updated 3.0 years ago by Michael Love 40k • written 3.0 years ago by aec ▴ 90

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1.4k

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limma dose-response linear model model formula

updated 5.5 years ago by James W. MacDonald 63k • written 5.5 years ago by biominer ▴ 10

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1.6k

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edgeR edger "glmqlftest()" timecourse model

updated 5.8 years ago by Ryan C. Thompson 7.8k • written 5.8 years ago by heikki.sarin ▴ 10

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1.8k

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egdeR multiple time points model.matrix differential exon usage model

5.8 years ago heikki.sarin ▴ 10

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1.0k

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dexseq timecourse model.matrix model

5.8 years ago heikki.sarin ▴ 10

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1.2k

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dexseq rna-seq model.matrix model

updated 5.9 years ago by Michael Love 40k • written 5.9 years ago by heikki.sarin ▴ 10

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1.1k

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EdgeR rank model

5.9 years ago philip.freda • 0

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1.4k

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deseq2 experimental design timecourse rnaseq model

updated 6.6 years ago by Michael Love 40k • written 6.6 years ago by athief ▴ 20

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692

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Deseq2 model

6.9 years ago jrivera • 0

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2.5k

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deseq2 model

updated 7.9 years ago by Simon Anders ★ 3.7k • written 7.9 years ago by da.de ▴ 20

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1.8k

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limma goodness fit linear model

updated 8.4 years ago by Gordon Smyth 47k • written 8.4 years ago by nonCodingGene ▴ 10

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8.2k

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DESeq2 linear model model

updated 2.1 years ago by Michael Love 40k • written 8.5 years ago by andrew.j.skelton73 ▴ 360

16 results • Page 1 of 1

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Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10

Sure, noted.

Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10

@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …

Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k

PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.

Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k

> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …

Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0

Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.

Votes

WGCNA coupled with differential expression analysis: question about baseline module detection

WGCNA with paired samples

Comment: Question on constructing design matrix and defining contrasts for analysis

Answer: Question on constructing design matrix and defining contrasts for analysis

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Teacher to James W. MacDonald 63k