Quasar Error

support
Quasar Error danielacgranato  2019-06-19
 

Dear,
I have just installed Quasar and I am getting an error message ( see attached) regarding some parameter that must be changed. Could you help me set the document so that I can run Quasar on Skyline. Thank you very much. Best, Daniela

 
 
Nick Shulman responded:  2019-06-19
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

The error that you are getting is:
Error in `colnames<-`(`*tmp*`, value = c("peptide", "sample", "replicate", :
  attempt to set 'colnames' on an object with less than two dimensions

I am not sure what that error means, but I might be able to give you more information if I reproduce the error myself.

I'm not much of a QuaSAR expert, so we might have to send you to the QuaSAR support board which is at https://skyline.ms/project/home/software/Skyline/tools/Support/QuaSAR/begin.view?

-- Nick
 
danielacgranato responded:  2019-06-19
Thank you very much for your reply. I have attached the document. Please let me know if you need any other information. Best, Daniela
 
danielacgranato responded:  2019-06-19
Dear Nick,
I was able to run Quasar and get some results but still I am getting an error for one of the peptides (see below) and it wasn´t able to generate de response curves file. Besides, I would like to confirm if in Quasar LOD and LOQ is calculated based on the response curve of one transition only. If so how is this transition chosen in regards to the other ones? Thank you very much. Best, Daniela

[1] Processing arguments ...
[1] >>> Processing part 1 of 1
[1] Initializing ...
[1] Running AuDIT ...
[1] Calculating LODs ...
[1] Calculating CVs ...
[1] Generating plots ...
Saving 7 x 7 in image
[1] Generating response curves ...
[1] Peptide: DLSSHQLNEFLAQTLQR
Error in order(tran.quality, decreasing = TRUE)[1:n.transitions] :
  only 0's may be mixed with negative subscripts
Calls: tryCatch ... tapply -> lapply -> FUN -> FUN -> plot.calibration.curve
Execution halted

Finished!
 
Nick Shulman responded:  2019-06-19
Daniela,

I think your first error might be happening because you have not filled in anything for the "SampleGroup" annotations for your replicates.
(When I step through the code in RStudio, it looks like it's trying to do something with the data from the SampleGroup column and ends up iterating zero times and so something ends up being null later on and that causes the error message).

I do not know what QuaSAR does or how it's supposed to work.

It sounds like you worked around the first error by making a change to your Skyline document. If you send me the new version of your Skyline document, I can try to see whether I can get this second error of yours to happen.
-- Nick
 
danielacgranato responded:  2019-06-24
Dear Nick,
Thank you very much. I was able to run Quasar, after I removed the iRT from the target document and after filling the SampleGroup. I am sending the skyline document again. I am getting an error in one of the peptides and Quasar is not generating the calibration curves. I appreciate very much if you can help me in this manner. Thank you very much. Best, Daniela.
[1] Generating response curves ...
[1] Peptide: DLSSHQLNEFLAQTLQR
Error in order(tran.quality, decreasing = TRUE)[1:n.transitions] :
  only 0's may be mixed with negative subscripts
Calls: tryCatch ... tapply -> lapply -> FUN -> FUN -> plot.calibration.curve
Execution halted
 
Nick Shulman responded:  2019-06-24
Daniela,

Can you send me your new .sky.zip file?
You can use the menu item in Skyline:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

-- Nick
 
danielacgranato responded:  2019-06-24
Dear Nick,
I have attached the zip file. thank you for your help. Best, Daniela
 
Nick Shulman responded:  2019-06-24
Daniela,

It looks like that "only 0's may be mixed with negative subscripts" error happens if you have not chosen a number for "Number of transitions to plot".

When you invoke QuaSAR in Skyline, the QuaSAR dialog comes up. On the "Plots" tab of that dialog, there's a dropdown "Number of transitions to plot" where you can choose a number between 1 and 6. Choosing any number will work, but if you leave it blank then you will get the error you're seeing.
-- Nick
 
danielacgranato responded:  2019-06-24
Thank you very much. Now it worked just fine. Best, Daniela.