Bioconductor 2-dye

Showing : 2-dye • reset

2

votes

3

replies

1.2k

views

limma 2-dye agilent common reference design

updated 8.0 years ago by James W. MacDonald 64k • written 8.0 years ago by Guido Hooiveld ★ 3.8k

2

votes

2

replies

1.2k

views

limma limma design matrix design and contrast matrix 2-dye

updated 8.1 years ago by Gordon Smyth 49k • written 8.1 years ago by Guido Hooiveld ★ 3.8k

2 results • Page 1 of 1

Recent ...

Replies

Comment: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k

> Is it okay to apply removeBatchEffect before a limma analysis(limma linear model)? No, you should not apply any batch correction before …

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

Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…

Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k

You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …

Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k

Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…

Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0

Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …

Votes

Answer: enrichGOgradient color change

Answer: Filter genes by expression for voomLmFit

Awards • All