Discrepancy between GUI options and R code output

[Yasmin Chau]

I tried out the GUI to generate the starting base code for running MSstats in a terminal (so I can use my university's cluster computational resources). I think there is discrepancy between the options I select at the data upload page and the default options that are selected in the R code that is generated at the end. 

Especially for: filter_with_Qvalue (default is TRUE in the R code but on GUI it is unchecked), removeProtein_with1Feature (default seems to be TRUE in the R code, but it's unchecked in the GUI).

I attached screenshots of my GUI screen to show those options, and I attached the resulting R code.