I am trying to use RUVSeq for normalising the RNA-Seq data. I would like to know if RUVSeq can take the pairing information of the sample as a factor for the normalisation.

From the documentation:

x <- as.factor(rep(c("Ctl", "Trt"), each=3))​
set <- newSeqExpressionSet(as.matrix(filtered), phenoData=data.frame(x,row.names=colnames(filtered)))
set1 <- RUVg(set, spikes, k=1)

Will it consider if I give the pairing information i.e each patient has two samples treated and ctrl.

x <- as.factor(c("Ctl","Trt","Ctl","Trt",Ctl","Trt") 
subject <- as.factor(rep(1:3,each=2))
design <- model.matrix(~subject+treat)
set <- newSeqExpressionSet(as.matrix(filtered),phenoData=data.frame(design,row.names =colnames(filtered)))
set1 <- RUVg(set, spikes, k=1)