I would need a bit of help please on SVA package for batch correction :
Assuming I have a matrix (let's call it DATA) of gene expression having 3 treatments (lets's say, CTRL, TREAT1, TREAT2), after correcting for batch effects in SVA, how could I obtain the matrix of CORRECTED VALUES ?
A piece of R code is :
DATA= as.matrix(gene.expression) ### here is the MATRIX DATA ;)
group = as.factor(rep(c("CTRL", "TREAT1", "TREAT2"), each=3))
mod1 = model.matrix(~group)
mod0 = cbind(mod1[,1])
svseq = svaseq(DATA, mod1, mod0, n.sv=1)
and I would need to obtain the matrix of CORRECTED_DATA ? thanks !