I want to use my own intensity file as the input of champ.CNA function. But I run into the error:

> cna=champ.CNA(loadFile = T, file = "intensity.txt", pd=targets, filterXY = F)
Run champ.CNA
Error in read.table(file, row.names = T, sep = "\t") :
  invalid 'row.names' specification

Clearly "row.names= T" is causing the problem. Could you fix this? Thanks!

I guess, because your file name and row names are same the function is giving the error.

Please try using a different name for your file.