Error message

Error message Wilf  2014-06-25 10:46

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

Could you help please.

All the best

Michael responded:  2014-06-25 11:53
Hi Andrew -

 My inclination is that there is an NA value somewhere in your results file. If there is an NA in the results file sprocop will not run. My suggestion would be to go to input..and look for any missing data points and fix them by either deleting or fixing the integration in skyline. Also if you are monitoring a 2+ and 3+ charge state from a single peptide you will get a similar error. just delete one of the charge states for that particular peptide. These will be fixed in the next version. Please let me know if one of these does not fix your problem.

Wilf responded:  2014-06-26 05:42
Hi Michael,

The error message was being generated because of the N/A, however I am now getting:

Error in dim(PA) = c(L, L2) :
  dims [product 236] do not match the length of object [288]
Calls: tryCatch -> tryCatchList -> parse.cmdline
Execution halted



Thanks for your help

Michael responded:  2014-06-26 05:46
Theres not a 2+ and 3+ charge state for a particular peptide? Could you zip the skyline file and email it to me? File - share Email address:

Michael responded:  2014-06-26 06:01
Hi Andrew

For each peptide there can be only one precursor form. If this is not the problem please send me the Skyline file and I will have a look. In the new version this will not be the case.