Bioconductor DesignMatrix

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limma DifferentialExpression Designmatrix

12 months ago Tadeoye ▴ 20

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571

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DESeq2 Designmatrix limma

updated 17 months ago by James W. MacDonald 68k • written 17 months ago by Neha • 0

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982

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subsettingdata edgeR designmatrix

updated 19 months ago by Gordon Smyth 53k • written 19 months ago by prity6459 • 0

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limma designmatrix

updated 20 months ago by Gordon Smyth 53k • written 20 months ago by avery • 0

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DESeq2 designmatrix edgeR limma tidybulk

updated 2.9 years ago by Michael Love 43k • written 2.9 years ago by aditya.m ▴ 10

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R designmatrix edgeR limma model.matrix

3.0 years ago Abdul ▴ 20

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DESeq2 limma modelmatrix edgeR designmatrix

updated 4.1 years ago by Gordon Smyth 53k • written 4.2 years ago by rebecca.lea.johnston • 0

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designmatrix deseq2 DESeq2

updated 4.1 years ago by swbarnes2 ★ 1.4k • written 4.1 years ago by OST • 0

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designmatrix RNA-seq limma

updated 4.7 years ago by Gordon Smyth 53k • written 4.7 years ago by athief ▴ 20

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997

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designmatrix DifferentialExpression edgeR RNAseq

4.8 years ago nageshprabhu.k ▴ 10

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MutlipleFactors DesignMatrix edgeR

4.8 years ago Debayan ▴ 20

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edgeR pairedsamples designmatrix

4.8 years ago sfidemw • 0

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deseq2 miRNASeq designmatrix Batch

updated 5.7 years ago by Michael Love 43k • written 5.7 years ago by anshulmbi • 0

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edger r differentialanalysis rnaseq designmatrix

updated 6.6 years ago by Aaron Lun ★ 29k • written 6.6 years ago by Beginner ▴ 60

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Limma designMatrix

updated 7.4 years ago by Aaron Lun ★ 29k • written 7.4 years ago by Keifa ▴ 10

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limma microarray designmatrix

updated 9.4 years ago by Aaron Lun ★ 29k • written 9.4 years ago by nashchem • 0

16 results • Page 1 of 1

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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k

It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …

Votes

C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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Commentator to sina.nassiri ▴ 130