Consider the following guidelines:

  • Read the ID column into the R script as a string, especially for the ID values from the Proteins table. As seen in previous figures the ID columns exported from any table in the Proteome Discoverer application are exported with quotes around them. The scripting language might unexpectedly modify IDs on import when reading them as a numeric value, which leads to errors when importing results back into the application.
  • Use the following options when using the read.table function to import the .csv files:
    - header = TRUE
    - check.names = FALSE
    - colClasses = character (This keeps the ID columns intact as described previously.)