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Hello!
I am using the vsn package to process Rat Gene 2.0 ST chips. I have to
export the data from xps and put the data into vsn as a matrix. The
data going into vsn has column names corresponding to "X" and "Y"
locations and the MEAN intensity for each sample.
I call vsn with ' fit <- vsn2(as.matrix(data[,3:ncol(data)]))' which
is then followed by the prediction step 'n_data <- predict(fit,
newdata=as.matrix(data[,3:ncol(data)]))'
Now the output data has no "X" or "Y" values and the row numbers start
at 660693. What is the standard method for keeping a unique
identifier for each row name throughout the vsn algorithm?
TIA
Matt