• Sign In
  1. Requests

Cannot correctly install MSstats to Skyline

support

View Request

view list print
Cannot correctly install MSstats to Skyline natbat  2018-08-07 02:40
 

Hello

I need MSstats for data analysis, but whatever I do to install it does not go correctly.

At first, MSstats was installed more or less, but when I tried to run QC, it gave the error message that
pwiz.Skyline.Model.Tools.ToolExecutionException: Error running the installed tool MSstats\QC. It seems to be missing a file. Please reinstall the tool and try again. ---> System.IO.FileNotFoundException: Could not load file or assembly 'file:///C:\Users\natbat\AppData\Local\Apps\2.0\KN6PMERL.PTM\1K88DWB8.VY9\skyl..tion_e4141a2a22107248_0003.0006_46da8c86f5903517\Tools\MSstats_external_3.6.1\MSStatArgsCollector.dll' or one of its dependencies. The system cannot find the file specified.
at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark)
at System.Reflection.Assembly.LoadFrom(String assemblyFile)

I tried to re-install MSstats. I went Tools --> Tool store --> MSstats --> Reinstall but it seems nothing happend. I am not even sure that oit was really un-installed and installed again. there was no messages confirming that.

Then I went to Tools --> External tools --> Menu contents, and Removed MSstats related tool. After that I went again to Tools --> Tool store --> MSstats, and pressed Install.
Something was installed. MSstats\Data processing, group compatrison and Design samle size appeared. But the QC option was missing.

Then I went to MacCoss lab site --> External tools and downloaded the zip file. However, when I try to extract files, it shows problems with encripting the files.

I do not understand what else can I do.
Please help, I need this tool for data analysis.

Sincerely
Natalia
 
 
Nick Shulman responded:  2018-08-07 11:06
Hi, Natalia,

It looks like the name of that menu item changed from "QC" to "Data Processing" back in June.
I do not know why that change was made, but I imagine that the functionality is still the same.
If the new menu item is behaving differently, you can ask about it on the MSstats support board:
https://groups.google.com/forum/#!forum/msstats

I am not sure what would be causing the error that you saw when you downloaded the .zip file. It's probably not worth looking into since you should just install the latest version of MSstats and use the "Data Processing" menu item. (If this error does keep happening and is causing problems, maybe you could post a screenshot of what the error looks like).

-- Nick
 
natbat responded:  2018-08-10 00:19
Dear Nick

I have wrote request for help to Meena Choi (MSstats), and here is her response:

If you have the issue in Skyline, Skyline support board is the better place that you can get feedback.
I think that you already posted in Skyline support board and Nick helped. I suggested to uninstall R and MSstats in Skyline and to re-install MSstats in Skyline.
-Meena

What I have done next:
Uninstalled all older versions of R and R 3.5.0
Re-installed MSstats from the Tool store in Skyline which installed R 3.5.0
and some other programs necessary for MSstats.
I attach here the log that appeared in the Immediate window in Skyline

After that I tried to run MSstats, the message what I have got is also attached.
Includes following:

Some DetectionQValue have no value. Please check "Result Grid" in View.
Error in runQC() :
 Can't finish analysis.

Please look into the installation log. There is the following info there which looks suspicious to me:

Warning messages:
The downloaded binary packages are in
    C:\Users\natbat\AppData\Local\Temp\RtmpUrTiTi\downloaded_packages
1: package 'grid' is not available (for R version 3.5.0)
2: package 'grid' is a base package, and should not be updated

Should it be like that?
Was everything OK with installation?

Because it could be that something is wrong with annotation, or I did something incorrectly in the Skyline file itself. I attached the Skyline file also.

Hope you will give me some advice what else I could do

Best regards
Natalia
 
Nick Shulman responded:  2018-08-10 02:34
You have successfully installed MSstats.
The error that you are getting is:
Some DetectionQValue have no value. Please check "Result Grid" in View.

That looks like a bug in the latest version of MSstats. I will email Meena and make sure she knows about it.

You will have better luck if you use the previous (June) version of MSstats which you can download from here:
https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=MSstats&version=3.13.2

After you download the zip file from that page ("MSstats_ext_tool_3.13.2b.zip"), you can install it in Skyline with the menu item:
Tools > External Tools > Add > From File...
 
natbat responded:  2018-08-10 03:24
Dear Nick

Yes, previous MSstats version works fine.
Thank you for your help very much indeed!

Best regards
Natalia