I think there is an error in the FBMN documentation in the section on using XCMS. The issue is here:
Process with XCMS
Export the results file for FBMN for GNPS
Option A. has the commands reversed.
In the step where you are exporting a 'feature quantification table', in R/XCMS the command should be write.table. Then, for the step where you are exporting 'MS/MS spectral summary file', in R/XCMS the command should be WriteMgfData.
The sample code on GitHub has it all correct, but I could not quite figure out where I was getting an error when I submitted things to GNPS.
Thanks. Krista
I think there is an error in the FBMN documentation in the section on using XCMS. The issue is here:
write.table
. Then, for the step where you are exporting 'MS/MS spectral summary file', in R/XCMS the command should beWriteMgfData
. The sample code on GitHub has it all correct, but I could not quite figure out where I was getting an error when I submitted things to GNPS. Thanks. Krista