Bioconductor Shrinkage

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shrinkage DifferentialExpression DESeq2

updated 19 months ago by ATpoint ★ 4.7k • written 19 months ago by Abir.khazaal ▴ 10

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1.2k

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shrinkage apeglm

2.9 years ago Frederik Ziebell ▴ 30

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3.0k

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deseq2 shrinkage

updated 2.3 years ago by Michael Love 43k • written 5.0 years ago by Nicolas Rosewick ▴ 20

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1.4k

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deseq2 shrinkage

updated 6.2 years ago by Michael Love 43k • written 6.2 years ago by vvi • 0

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4.5k

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deseq2 betaPrior shrinkage significance

6.8 years ago brynedal ▴ 40

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1.6k

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deseq2 log2fc shrinkage

updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by aec ▴ 90

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Comment: DepMap data mismatch by Laurent Gatto 1.6k

It might be due to different versions. The repacked/cleaned data in the `depmap` R/Bioconductor package is old, but the latest files can al…

Comment: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k

If you are using `conumee2`, then you are in the wrong place. That isn't a Bioconductor package (yet? No idea if they have/will submit it).

Answer: myvariant error by James W. MacDonald 68k

You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for yo…

Answer: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k

There doesn't appear to be a function called `CNV.summaryplot` in `conumee`. What package does that function come from?

Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …

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A: What is the "linear model" part used for in Limma?

Comment: Use of limma R package with targeted proteomics for DE analysis

A: Unbalanced experiment with multiple samples from each patient.

Unbalanced experiment with multiple samples from each patient.

Answer: Vertical line at A=0, nothing else, on MA plot

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