SProCoP Support 

Welcome to the SProCoP support board. If you have a question about using SProCoP, or if you encounter a problem, you can post your questions here.

Support is provided by the creators of the software, as time allows, though we hope others will share their experience as the user community grows.

In order to post to the forum, you'll need to sign up for an account. If you already have an account but have forgotten your password, you can reset your password using the "Forgot your password?" link on the Sign-in page.

When you post a question, please include the following information:

  • Your operating system, the version of the software you are using, and any other information that may help us to answer your question
  • A detailed description of your problem or question, including instructions for re-creating any problem that you are encountering

If you are including text output from a tool, please attach files to your message, rather than pasting in long text.


Requests 
Showing: all requestss
Question about SProCop
(2 responses) fazeliniah 2017-09-11
Hi Skyline team,
I have been trying to use SProCop for a PRM project. Unfortunately I get the following error. Any thoughts? I have attached the .sky file.
Thanks
Hossein

1>Error in dim(PA) = c(L, L2) :
1> dims [product 170] do not match the length of object [79]
1>Calls: tryCatch -> tryCatchList -> parse.cmdline
1>Execution halted
1>
1>Finished!
 HI_PRM_4samples.sky 
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SProCoP Support - R already installed
Carlo.Martins 2016-07-26
Hi all,
I am trying to install SProCoP in one of my company's computer.
As R is already installed, I wouldn't like to have to call IT support to install it again (they wouldn't understand a second installation requirement for the same software).
So, my question is: is it possible to override R installation and go ahead with SProCoP?

Thanks,
Carlo
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SProCoP Error-Skyline V 3.5
(5 responses) rick.king 2016-03-11
Hi,

I am getting the following error when trying to use SProCoP with Skyline V 3.5 (R 3.0.2):

Error in dim(PA) = c(L, L2) :
  dims [product 72] do not match the length of object [144]
Calls: tryCatch -> tryCatchList -> parse.cmdline
Execution halted


Finished!

Operating System:
Windows 7 Professional (64-bit)


Attached is the skyline file that is causing the error.

Thanks for your help.
Sue and Rick
 Human Apo_13C15N Master Mix 4 w TracerIons-SProCoP-Test-11Mar16.zip 
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Indicating the centroided mass in 'full scan' viewer
r bagshaw 2015-05-13
Hi,
For untargeted small molecule work, it would be handy when one clicks on the chromatogram trace to show the MS scan spectrum that the mass of the monoisotopic peak is displayed above the peak (kind of like what happens in xcalibur). Maybe there are options for number of decimal places, maybe even chemical composition? Right now to obtain the actual mass, I have to zoom in quite closely to get the x-axis to display the m/z to 4 or 5 decimal places and then read the mass from there.
Thanks!
--Rick
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Error message
(1 response) sstoychev 2015-04-03
Hi,

I get the following error message when running SProCoP via Skyline:

Error in dim(PA) = c(L, L2) :
  dims [product 210] do not match the length of object [240]
Calls: tryCatch -> tryCatchList -> parse.cmdline
Execution halted


Finished!

Regards,

Stoyan
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Error message
(1 response) jerome_vialaret 2014-11-24
I try to use SProCoP1.0 on my QTOF PRM data with Skyline 2.6.0.6851
The external tool is easly install and I could generate SProCoP report but when I run SProCoP tool I have this error message:

Error in colMeans(PA[1:Q1, ]) :
  'x' must be an array of at least two dimensions
Calls: tryCatch -> tryCatchList -> parse.cmdline -> colMeans
Execution halted
Finished!



Jerome
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Error message when loading in new result file
(2 responses) MWidya 2014-10-28
Hi,

I've just started exploring SProCop to analyse our QC samples and am having trouble getting it to work sometimes. I've successfully loaded and analysed a few test files, but as soon as I try using a different data set (using the same settings) or loading in a few new result files into a file that worked before I get an error message:

1>Error in dim(PA) = c(L, L2) :
1> dims [product 126] do not match the length of object [105]
1>Calls: tryCatch -> tryCatchList -> parse.cmdline
1>Execution halted
1>
1>Finished!
1>
 
Another error message I keep encountering is:

Error in plot.window(...) : need finite 'ylim' values
Calls: tryCatch ... parse.cmdline -> plot -> plot.default -> localWindow -> plot.window
Execution halted
Finished

It's probably something incredibly obvious that I'm missing, but could you point me in the right direction?

Thanks!
Kind regards,
Marcy
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Using SProCoP with SRM data?
(7 responses) andre 2014-08-17
Hi Michael,

I tried using SProCoP with an SRM data set (two traces for the analyte and one trace for the internal standard) acquired on an ABI Sciex 5500 QTRAP and couldn't make it work; when checking the SProCoP input file I noticed that the mass error column shows N/A entries. Is this a general issue with SRM data?

Best regards,
Andre
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Error message.
(1 response) cmhende 2014-07-10
Hello,

I keep getting the same error message when I attempt to execute SProCoP from the Tools menu. I cannot seem to figure out what I am doing wrong. Could you possibly point me in the right direction? The error message is below.
 
Error in plot.new() : figure margins too large
1>Calls: tryCatch ... tryCatchList -> parse.cmdline -> plot -> plot.default -> plot.new
1>Execution halted
1>
1>Finished!


Thank you very much for your help!

Best,
Clark
Operating system: Windows 7 (32-bit)
Skyline version: Skyline-daily 2.5.16347
SProCop version: 1.0
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Error message
(4 responses) Wilf 2014-06-25
Hi,

I think I am doing something silly. I am wanting to use SProCoP and keep getting the following error message:
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
  line 285 did not have 8 elements
Calls: tryCatch ... tryCatchList -> parse.cmdline -> read.table -> scan
Execution halted
Finished!

Could you help please.

All the best

Andrew
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discuss page - SProCoP Support
(1 response) brian flatley 2014-03-04
Hi,

How does SProCoP decide which runs to use to calculate threshold values
e.g. If I select 3 (and I have load 20 files) how does it select which three to use as a calculator?

Thanks,

Brian

Operating System - Windows 8
Skyline Version - 2.5.0.5675
SProCoP Version - 1.0
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