Hello,

I have XMS data files from a Scion GC-MS that I converted in netCDF. I would like to do some data preprocessing before any statistical analysis by using MSnbase and XCMS libraries.

When I use the readMSData from MSnbase on my CDF files, I get this warning: "Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method." I thought at first that I could set the polarity in the object afterwards but the function get stuck at this step.

If someone have a solution for that or to convert my XMS files into the recommended mzXML format, thank you.

Best regards, Julien Kermorvant

Dear Julien,

firstly, polarity is not really required for xcms data analysis, you should just make sure to just analyze samples measured with the same polarity. If you want to set the polarity you could do that with:

fData(data)$polarity <- 0L

Where data is the object you got from readMSData. The polarity encoding is 0L for negative polarity, 1L for positive polarity.

cheers, jo