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CCMS-UCSD / GNPSDocumentation

Documentation for GNPS and related tools as written in mkdocs
https://ccms-ucsd.github.io/GNPSDocumentation/
MIT License
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FBMN documentation for XCMS #264

Closed redbluewater closed 4 years ago

redbluewater commented 4 years ago

I think there is an error in the FBMN documentation in the section on using XCMS. The issue is here:

  1. Process with XCMS
  2. 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