Bioconductor Blocking

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3.6k

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limma edger blocking paired samples

updated 5.4 years ago by Gordon Smyth 50k • written 5.4 years ago by anou ▴ 10

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1.9k

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limma repeated measurements blocking random effects

updated 4.1 years ago by Gordon Smyth 50k • written 4.2 years ago by Jane ▴ 10

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1.4k

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edger limma paired blocking ruvseq

updated 3.9 years ago by Gordon Smyth 50k • written 3.9 years ago by ScA • 0

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921

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diffbind blocking model

updated 3.5 years ago by Rory Stark ★ 5.1k • written 4.5 years ago by melnuesch ▴ 10

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806

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diffbind differential binding analysis blocking

updated 6.3 years ago by Rory Stark ★ 5.1k • written 6.3 years ago by zhangly811 • 0

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692

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edgeR blocking

updated 3.0 years ago by Yunshun Chen ▴ 840 • written 3.0 years ago by Molly • 0

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685

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voom blocking limma

updated 6 months ago by Gordon Smyth 50k • written 6 months ago by Gerhard Thallinger ▴ 180

7 results • Page 1 of 1

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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

How am i making the data? I am using the DESeq2 output data which I had generated

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k

Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …

Answer: Citation for edgeR user guide by Gordon Smyth 50k

Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You are just making up data? What is the point of this exercise?

Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k

What do you mean by 'the information'? Do you have things in particular that you want?

Votes

Answer: Citation for edgeR user guide

Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)

Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.

Answer: minfi::read.metharray.exp

Comment: Trying to use enrichGO

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