Bioconductor Pipeline

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pipeline testdata ChAMP

updated 12 months ago by James W. MacDonald 64k • written 12 months ago by luisfranciscoteves • 0

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scRNAseq Pipeline Seurat SingleCellExperiment

4.1 years ago albadrs.93 ▴ 10

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illumina human ht-12 v4 limma pipeline

7.3 years ago alakatos ▴ 130

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docker annotation pipeline

7.6 years ago Elena Grassi ▴ 10

4 results • Page 1 of 1

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Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0

I see. Do you recommend a certain method to get norm.factors through calcNormFactors function espcially if the downstream analysis includes…

Comment: Can the limma package be applied to Log2 RUV-normalized data? by Gordon Smyth 49k

515 samples is certainly large enough.

Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0

Thank you for your kind response Gordon! :) Have a good time at the end of the year! Best, Yujin Kim

Comment: Agilent Microarray Gene Oncology analysis gone wrong by SamGG ▴ 320

Gordon said to let coef to its default value: topTable(fit, n=20)

Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0

Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…

Votes

Comment: Can the limma package be applied to Log2 RUV-normalized data?

Answer: Correct the batch effect in methylation analysis in R

Comment: Why is DMRcate not available for Bioconductor version 3.18?

Answer: Correct the batch effect in methylation analysis in R

Awards • All

Scholar to Gordon Smyth 49k

Popular Question to Lluís Revilla Sancho ▴ 720

Popular Question to Frederik Ziebell ▴ 20