Question: ReadMSData problem with xcms
gravatar for bhgyu
2.1 years ago by
bhgyu30 wrote:


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
xcms readmsdata • 1.1k views
ADD COMMENTlink modified 2.1 years ago by Johannes Rainer1.5k • written 2.1 years ago by bhgyu30
Answer: ReadMSData problem with xcms
gravatar for Johannes Rainer
2.1 years ago by
Johannes Rainer1.5k
Johannes Rainer1.5k wrote:

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

ADD COMMENTlink written 2.1 years ago by Johannes Rainer1.5k

Worked perfectly! Thanks so much Johannes!

ADD REPLYlink written 2.1 years ago by bhgyu30
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