Bioconductor Complex-design

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limma complex-design paired design

updated 7.7 years ago by Aaron Lun ★ 29k • written 7.7 years ago by ML18 ▴ 10

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3.0k

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rnaseqpower sspa sample size sequencing complex-design

updated 9.8 years ago by m.van_iterson ▴ 20 • written 9.8 years ago by roser.navarro • 0

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6.9k

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limma paired samples complex-design

10.0 years ago • updated 9.9 years ago aec ▴ 90

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4.8k

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limma model matrix limma design matrix complex-design

updated 10.5 years ago by Aaron Lun ★ 29k • written 10.5 years ago by Guido Hooiveld ★ 4.1k

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3.3k

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deseq2 multiple factor design complex-design

updated 10.7 years ago by Michael Love 43k • written 10.7 years ago by sifujio • 0

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7.4k

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combat software error rnaseq complex-design

updated 11.1 years ago by Peter Langfelder ★ 3.0k • written 11.1 years ago by Stefano Mangiola ▴ 40

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2.9k

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edgeR complex-design

updated 11.1 years ago by James W. MacDonald 68k • written 11.1 years ago by lwc628 ▴ 20

7 results • Page 1 of 1

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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/

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0

Thank you very much! will take that into consideration

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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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Popular Question to jared.andrews07 ▴ 30

Popular Question to James W. MacDonald 68k