Errors when running tutorial wildsmith.kristin  2014-04-21
 
I am running through the Quasar tutorial with some colleagues and we are running into a couple problems with which i hope you can help. We have all just installed the Quasar tool in skyline and have encountered errors.
1.On my PC, Quasar give an error message (slide 1) that the required columns are missing, however, the results grid is complete.

2.On the second slide, all of us are missing the "standard present" box, and for my other 2 colleagues, Quasar runs, but no response curves are generated possibly due to an error with a specific peptide (see slide 3). We attempted to delete this peptide, but actually can't find it. It appears that all other plots and csv files were generated.
Do you have any suggestions for us?
 
 
wildsmith.kristin responded:  2014-04-21
for 2. we found a link in a separate thread and installed Quasar 1.2. (http://www.broadinstitute.org/~manidr/QuaSAR-1_2.zip. )We now see the "standard present" box, and the response curves were successfully generated.

I encountered the "required columns" are missing error again, unfortunately.
 
minliecn responded:  2015-07-12
I am practicing the QuaSAR tutorial with Skyline V3.1 and QuaSAR1_32. I have encountered the same errors as listed in the third ppt slide by Kristin. Does anyone has a solution for the issue? Thanks!
 
Mani responded:  2015-07-13
I think this error is caused by an incorrect default for the "Number of transitions to plot" in the "Plots" tab. If you manually select a number of transitions to display (3 is a good default), this error should go away. I'll soon release a new version with this problem fixed.
 
minliecn responded:  2015-07-13
Thanks for your help, Mani. I have a different question now. when I am trying to play with my own dataset, skyline was complaining about "Error in calculate(data.subset, concentrationFile, output.prefix = outputPrefix, :
   No data for LOD calculation -- disable LOD calculation". Do you know which part is causing this issue? Thanks very much for your help.
 
Mani responded:  2015-07-13
As the error message points out, QuaSAR is not able to calculate LODs using your data. This could be because there are no blank samples (with concentration = 0), or not enough replicates to calculate standard deviations. If you uncheck the "LOD/LOQ table" checkbox, the error should go away. Obviously, you won't get LOD/LOQ tables, but calibration curves and CV values will be output. If the error persists, may be you can send me the data (as an export, or as a Skyline file) so I can try to debug the problem.