Bioconductor Model design

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deseq2 rnaseq model design

7.0 years ago • updated 6.9 years ago swillis4 ▴ 10

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deseq2 model design differential gene expression experimental design

updated 7.9 years ago by Michael Love 43k • written 7.9 years ago by L_K • 0

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deseq2 multiple time points time course casecontrol model design

updated 8 months ago by wuwenhui2 • 0 • written 8.4 years ago by heikki.sarin ▴ 10

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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 …

Comment: problem reading bam files into nucleR by efoss ▴ 10

I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…

Answer: two questions about limma by Gordon Smyth 53k

Answered here: https://support.bioconductor.org/p/16318/

Votes

C: DESeq2 Following RSEM

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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Commentator to sina.nassiri ▴ 130