Entering edit mode
8.8 years ago
GouthamAtla
12k
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)