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minfiDataEPIC arrays limma minfi Epigenetics

updated 3.4 years ago by Gordon Smyth 50k • written 3.4 years ago by Jeff ▴ 20

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minfiData plotsex minfi minfiDataEPIC r

updated 3.2 years ago by suman • 0 • written 3.2 years ago by Bethan • 0

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minfiDataEPIC EpicV2

updated 7 months ago by Zuguang Gu ▴ 260 • written 8 months ago by Izabela.ams • 0

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minfiDataEPIC minfi

updated 8 months ago by James W. MacDonald 65k • written 8 months ago by phelankj • 0

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Annotation annotate DifferentialMethylation minfiDataEPIC

updated 7 months ago by Basti ▴ 780 • written 7 months ago by titangerd • 0

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minfiDataEPIC #SexPrediction minfi

updated 2.6 years ago by Basti ▴ 780 • written 2.6 years ago by nucasa • 0

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minfiDataEPIC methylationArrayAnalysis

updated 9 months ago by ATpoint ★ 4.0k • written 9 months ago by rae.alshammari ▴ 10

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Quantile noob Normalization minfi minfiDataEPIC

updated 20 months ago by James W. MacDonald 65k • written 20 months ago by mikat • 0

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methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray

updated 12 months ago by Gordon Smyth 50k • written 13 months ago by Grace • 0

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minfiDataEPIC minfi

updated 5 months ago by Basti ▴ 780 • written 5 months ago by Ana • 0

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minfi minfiDataEPIC

6 weeks ago Felix • 0

11 results • Page 1 of 1

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Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Votes

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0