Bioconductor Designmatrix

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R designmatrix edgeR limma model.matrix

16 months ago Abdul ▴ 20

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designmatrix RNA-seq limma

updated 3.1 years ago by Gordon Smyth 50k • written 3.1 years ago by athief ▴ 20

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DESeq2 limma modelmatrix edgeR designmatrix

updated 2.5 years ago by Gordon Smyth 50k • written 2.5 years ago by rebecca.lea.johnston • 0

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678

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deseq2 miRNASeq designmatrix Batch

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by anshulmbi • 0

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886

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edgeR pairedsamples designmatrix

3.2 years ago sfidemw • 0

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933

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MutlipleFactors DesignMatrix edgeR

3.2 years ago Debayan ▴ 20

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999

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DESeq2 designmatrix edgeR limma tidybulk

updated 15 months ago by Michael Love 41k • written 15 months ago by aditya.m ▴ 10

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1.1k

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Limma designMatrix

updated 5.8 years ago by Aaron Lun ★ 28k • written 5.8 years ago by Keifa ▴ 10

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841

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edger r differentialanalysis rnaseq designmatrix

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by Beginner ▴ 60

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limma microarray designmatrix

updated 7.7 years ago by Aaron Lun ★ 28k • written 7.7 years ago by nashchem • 0

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128

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subsettingdata edgeR designmatrix

updated 6 days ago by Gordon Smyth 50k • written 6 days ago by prity6459 • 0

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designmatrix deseq2 DESeq2

updated 2.5 years ago by swbarnes2 ★ 1.3k • written 2.5 years ago by OST • 0

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145

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limma designmatrix

updated 19 days ago by Gordon Smyth 50k • written 19 days ago by avery • 0

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615

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designmatrix DifferentialExpression edgeR RNAseq

3.2 years ago nageshprabhu.k ▴ 10

14 results • Page 1 of 1

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre

Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…

Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0