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. 

[Anthony Wu]

Hi,

May I ask which version of MSstatsShiny are you using?  I believe this issue was fixed in the most recent release (Release 3.23, MSstatsShiny 1.14.0, R 4.6.0).  If you're using an older version, could you update to the latest version and let me know if you still see any discrepancies?

Thanks,

Tony

[Yasmin Chau]

Hi Tony,

I am indeed using the latest release, release 3.23 with MSstats Shiny 1.14.0 and with R 4.6.0. The results I shared came from those releases. 

Either way, for my current use I can change the settings as I like once I run it on the terminal. Are the default settings in the manual still the recommended default settings to use?

Best,

Yasmin