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Skyline crashes: Regression - Score to run

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Skyline crashes: Regression - Score to run gpimienta  2018-08-15 15:05
 

I am all of the sudden having trouble with Skyline every time I try running a Regression - Score to run calculation. Skyline crashes. I have uninstalled and re-installed it. I also have the latest version.
Skyline seems to be having trouble interacting with Windows according to the message given. Problem event name: AppHangB1.
Any help with this?
Thanks,
Genaro
 
 
Nick Shulman responded:  2018-08-15 15:32
Can you send us your Skyline document?

In Skyline you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files, including extracted chromatograms.

If that .zip file is less than 50MB then you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

Can you also send us your Skyline Settings?
The way that you export your Skyline settings is to first do:
Settings > Save Current
and then give the settings a name (doesn't matter what name).

Then, after you have given the settings a name, you can then use the menu item:
Settings > Share
to save the settings out to a .skys file.
Please attach that .skys file to this support request.

I believe when you bring up that Score to Run regression window, Skyline goes through all of the retention time predictors that it knows about, and tries to find the one that best fits your data. It sounds like one of these calculators is taking forever, and that calculator might either be saved in your Skyline document, or the .skys file.
(I believe we have some plans to make this Regression window much faster in the next version of Skyline).
-- Nick
 
Brendan MacLean responded:  2018-08-15 21:07

Is this a very large file? You can reduce the amount of work Skyline has to do by opening a file with fewer targets and replicates and doing the following:

  1. View > Retention Times > Regression > Score to Run
  2. Right-click in the plot, choose Calculator and select the single calculator by name you want to see with this document (or any calculator actually)
  3. Right-click in the plot, choose Model and make sure Linear is selected
  4. Right-click in the plot, choose Replicate and click Single

Worst case for time required to calculate the regression would be Calculator = Auto, Model = Lowess or KDE, Replicate = All. And, unfortunately, yes, this graph can end up blocking the UI while it does its calculation. We know this and as Nick indicates, Tobi now has code that both makes the calculations on multiple threads and avoids blocking the UI while it does that. This should make it both faster and not cause the "hang" you are seeing.

It is quite possible that if you are willing to wait long enough that the calculation will complete eventually and display the desired plot. Turing off auto-calculation for the calculator (also mentioned by Nick) is your first best bet. Then making sure you are not trying to do one of the more complex regression models.

Hope this helps. Though, we would also appreciate having a look at the files Nick requested. Thanks for posting the issue here.

--Brendan
 
gpimienta responded:  2018-08-17 13:14

Hi Nick and Brendan.
Thanks so much for you reply. I tried turning off "autocalculate", but the problem persisted. I could get a regression only when having one replicate (two technical replicate) uploaded, instead of the a total of four replicates.
I send attached the files requested. Please let me know if there is something in my settings that I ought to change for the "Score to run" function to work with all my files uploaded.
Genaro
 
gpimienta responded:  2018-08-17 13:15

Hi Nick and Brendan.
Thanks so much for you reply. I tried turning off "autocalculate", but the problem persisted. I could get a regression only when having one replicate (two technical replicate) uploaded, instead of the a total of four replicates.
I send attached the files requested. Please let me know if there is something in my settings that I ought to change for the "Score to run" function to work with all my files uploaded.
Genaro
 
gpimienta responded:  2018-08-17 13:16

Hi Nick and Brendan.
Thanks so much for you reply. I tried turning off "autocalculate", but the problem persisted. I could get a regression only when having one replicate (two technical replicate) uploaded, instead of the a total of four replicates.
I send attached the files requested. Please let me know if there is something in my settings that I ought to change for the "Score to run" function to work with all my files uploaded.
Genaro
p.s. there is an error when I send this message with my two files attached. I am sending here the settings. Will send the *.zip in another message.
 
gpimienta responded:  2018-08-17 13:17

Sending my Skyline session zipped.