SkylineRunner.exe to export mProphet Features

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SkylineRunner.exe to export mProphet Features s26guan  2020-06-25
 

Dear Skyline team,

Can you show me the export option for mProphet features? I tried --report-name="mProphet Features" and it was not working.

Got error: "Error: The report mProphet Features does not exist. If it has spaces in its name, use "double quotes" around the entire list of command parameters."

Many thanks.

 
 
Nick Shulman responded:  2020-06-25
There is no way to export mProphet features using the command line.
It would probably be straightforward for us to implement command line support for this. I do not think anyone has asked for this.
We might have imagined that exporting the mProphet features would only be used by for debugging purposes when the mProphet model was not behaving the way that you expected.

-- Nick
 
s26guan responded:  2020-06-25
Hi, Nick,

I hope to get some statistics of the q-values or p-values of extracted peptides, before feeding into the later stage of the pipeline. Is there an alternative to get the info with command line?

Thank you.
 
s26guan responded:  2020-06-25
Hi, Nick,

If there were none else interested, could we discuss in private and collaborate? Thank you.
 
Nick Shulman responded:  2020-06-25
There are two columns on the "Precursor Result" in the Document Grid:
Detection Q Value
Detection Z Score

When you apply an mProphet model to your Skyline document, those columns will have the values from the mProphet model.

-- Nick
 
Brendan MacLean responded:  2020-06-25
It sounds like you may just want to create your own custom report template with Detection Q Value and Detection Z Score in it.

You can consult the Custom and Live Reports tutorial on how to do this.

Exporting mProphet features is more for getting access to the individual feature scores used in mProphet training. This was originally implemented to allow us to run the original mProphet implementation in R and compare the results with our implementation in Skyline written in C#.

I think you are likely heading down the wrong track. Please explain in more detail what you have in mind if you think you really need these subscores or you see some value here which you cannot get in a custom report that you feel you need.
 
s26guan responded:  2020-06-25
Nick and Brendan,

Indeed, I am not very familiar with the report content. Please let me learn more of the Document Grid and that seems giving me the information I need.

Many thanks.