[BioC] VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?

Thornton, Matthew Matthew.Thornton at med.usc.edu
Fri Mar 7 00:25:50 CET 2014


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?



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