Re: File conversion for XCMS
Reply #3 –
You need to figure out which of the 3 files you need. Mixing different functions will likely mess things up.
Since you have Databridge I guess you have masslynx. So open a chromatogram --> display --> TIC. Here you have the functions listed and you can get the TIC of each function.
If that doesn't clear it up either ask the people that did the experiment or try to decipher the _extern.inf in the raw folders. That contains all the experiment settings and have sections for each function. The format is not very consistent between versions but I just checked and it seems MSe functions will have things like
Transfer MS Collision Energy Low (eV) 10.0
Transfer MS Collision Energy High (eV) 40.0
listed at least in my files.
What do you mean by "load the files with XCMS"? Using xcmsSet? How heavy this is depends on the settings. What happens? You run out of memory? At which point? How large are the files? Maybe they are not centroided?