Allow different validation methods when creating projects

[umutcakir]

Hello,

I want to use local FDR instead of global FDR to generate reports. Because the project file is too big, I cannot change from the validation tab in the graphical user interface. I have to use from the command line. I have two questions:

Can I change protein identifications based on local FDR when the project was already created with global FDR?

How can I set local FDR when I am generating identification parameters? In the old post, it is written “using the "Validation Parameters" in the advanced parameters”, but I cannot find validation parameters. I am using the recent version and does its name changed?

Umut

[mvaudel]

Hi,

Apologies for the delay of our answer. I am sorry but this option is currently not available via command line. We will look into implementing it but cannot give you an ETA at this stage. In the meantime, I recommend to export all hits (either by unchecking the "Validated Only" in the report settings or by using and FDR of 100%). Then you can filter by confidence, which is the same as a local FDR.

Hope it helps,

Marc