Hello, 

I cannot work out how to make the readMSData function work?

I get an error message. Anyone had this before and know how to solve it? Cheers!

temp = list.files(pattern="*.CDF")

readMSData(temp, pdata = pheno)
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Error in readMSData(temp, pdata = pheno) : 
  No MS(n>1) spectra in file meta1.CDF

readMSData with mode = "inMem" (the default) will by default read only MS level >= 2 from the input files. If you are going to use xcms you should use readMSData(temp, pdata = pheno, mode = "onDisk") which will a) read all MS levels from the input file and b) return a OnDiskMSnExp object that you need for xcms. OnDiskMSnExp objects don't read the full MS data into memory and are thus lightweight.

cheers, jo