Hi,

I was exploring batch effects in my data. At this stage, I don't want to introduce the 'variable of interest' (i.e. 'cancer' in the vignette/example given in sva.pdf that is used to get 'mod' - the model matrix). Should I use the mod0 matrix (i.e. the NULL matrix) as an input to the ComBat function (and get combat_edata2)? Will this correctly reflect the expression data corrected for batch effects?


###### Code #####

library(sva) 
library(bladderbatch)
data(bladderdata)
library(pamr)
library(limma)

pheno = pData(bladderEset)
edata = exprs(bladderEset)
mod = model.matrix(~as.factor(cancer), data=pheno) 
mod0 = model.matrix(~1,data=pheno)

batch0 <- c(rep(1,12),rep(2,15),rep(3,30))

## use mod
combat_edata = ComBat(dat=edata, batch=batch, mod=mod, numCovs=NULL, par.prior=TRUE) 


### use mod0
combat_edata2 = ComBat(dat=edata, batch=batch0, mod=mod0, numCovs=NULL, par.prior=TRUE)


##################


thanks!

	[[alternative HTML version deleted]]

