Bioconductor Complex-design

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limma complex-design paired design

updated 7.1 years ago by Aaron Lun ★ 28k • written 7.1 years ago by ML18 ▴ 10

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rnaseqpower sspa sample size sequencing complex-design

updated 9.2 years ago by m.van_iterson ▴ 20 • written 9.2 years ago by roser.navarro • 0

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limma paired samples complex-design

9.3 years ago aec ▴ 90

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limma model matrix limma design matrix complex-design

updated 9.9 years ago by Aaron Lun ★ 28k • written 9.9 years ago by Guido Hooiveld ★ 4.1k

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deseq2 multiple factor design complex-design

updated 10.1 years ago by Michael Love 43k • written 10.1 years ago by sifujio • 0

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combat software error rnaseq complex-design

updated 10.5 years ago by Peter Langfelder ★ 3.0k • written 10.5 years ago by Stefano Mangiola ▴ 40

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edgeR complex-design

updated 10.5 years ago by James W. MacDonald 68k • written 10.5 years ago by lwc628 ▴ 20

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Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0

There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…

Comment: Differing results with DESeq2 by JKim • 0

My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…

Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k

This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…

Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80

Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…

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remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

A: Unbalanced experiment with multiple samples from each patient.

A: Understanding contrasts limma

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