Bioconductor Nested

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DESeq2 multifactorial nested

updated 2.7 years ago by Basti ▴ 780 • written 2.7 years ago by jd • 0

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1.7k

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nested DESeq2

updated 3.8 years ago by Michael Love 43k • written 4.0 years ago by yampolsk • 0

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deseq2 Phyloseq Nested

updated 5.7 years ago by Michael Love 43k • written 5.7 years ago by mpuli011 • 0

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1.3k

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deseq2 Paired Nested

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by julia.chariker ▴ 10

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1.5k

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deseq2 nested de

updated 6.0 years ago by Michael Love 43k • written 6.0 years ago by gaio.transposon • 0

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1.8k

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edgeR nested glm glmQLFit

updated 6.6 years ago by Aaron Lun ★ 29k • written 6.6 years ago by jcalis ▴ 10

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edger nested design matrix differential expression

updated 10.8 years ago by Aaron Lun ★ 29k • written 10.8 years ago by Mauve • 0

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edger nested estimatedispersions

10.8 years ago Mauve • 0

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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