Chapter 2 🖎🏻 Batch Effect Correction

2.1 Batch Correction Method

Name	Algorithm	Data type
Combat	empirical Bayes frameworks	cleaned and normalized data
Combat_seq	negative binomial regression	count data
limma	linear model	log transfered data
DWD	distance weighted discrimination	all kinds of data

library(tigeR)
library(tigeR.data)
library(SummarizedExperiment)
SE <- cbind(MEL_GSE145996,MEL_GSE78220) 
SE_Combat <- remove_BE(SE,method = "Combat")
SE_Combat_seq <- remove_BE(SE,method = "Combat_seq")
SE_limma <- remove_BE(SE,method = "limma")
SE_DWD <- remove_BE(SE,method = "DWD")

SE_batch <- browse_BE(SE) + ggtitle("Origin")
Combat_batch <- browse_BE(SE_Combat) + ggtitle("Combat")
CombatSQ_batch <- browse_BE(SE_Combat_seq) + ggtitle("Combat_seq")
limma_batch <- browse_BE(SE_limma) + ggtitle("limma")
gridExtra::grid.arrange(grobs=list(SE_batch,Combat_batch,
                                   CombatSQ_batch,limma_batch))