help with multiple batch effects
€8 EUR
착불
Hello, I have an expression matrix of 1208 samples (1095 tumor and 113 normal) downloaded from TCGA. I know there are 3 batch effects: type, plateId and TSS. These batches are suggested from [login to view URL] . I've tried to correct for them with Combat but I need a little help with the model.matrix.
This is my code:
batch<[login to view URL](cbind(samples,plateId,group,TSS),as.is=T)[,-1]
##correct for group: group is 01 for tumor and 11 for normal
mod.1<- [login to view URL](~plateId+TSS, data=batch)
bat.1<- ComBat(dat=dati, batch$group, mod.1, [login to view URL] = TRUE, par.prior=TRUE, prior.plots=FALSE)
##correct for plateId
mod.2<- [login to view URL](~group+TSS, data=batch)
bat.2<- ComBat(dat=bat.1, batch$plateId, mod.2, [login to view URL] = TRUE,par.prior=TRUE, prior.plots=FALSE)
##correct for TSS
mod.3<- [login to view URL](~group+plateId, data=batch)
bat.3<- ComBat(dat=bat.2, batch$TSS, mod.3, [login to view URL] = TRUE,par.prior=TRUE, prior.plots=FALSE)
프로젝트 ID: #17253754
