Hi all,
I'm doing a metabolite discovery project. I've run some samples through LC/MS and am now analysing data with help of XCMS online.
I'm primarily a microbiologist, so stats is fairly often still a foreign language to me. XCMS produces both PCA and NMDS plots for showing sample metabolite variety, but I can't quite understand what the reason for any differences between the two plot types is. Can anyone explain the difference, or direct me to a stats-for-dummies/biologists resource that does?
Thanks!
You might look at MZmine (open source alternative to XCMS). They do all the same things and have an online manual that explains things far better than XCMS does. XCMS is based on the open-source stats package R, which assumes that you have a PhD in statistics before you start using it. If you are new to LC/MS you might also want to look at: https://www.researchgate.net/publication/315874699_Mass_Spectral_Data_Processing. There are a lot of issues that you need to deal with correctly BEFORE you get to XCMS.
Method Mass Spectral Data Processing
Hi Luke,
Thanks for the link. I'll have a readthrough - most of my data processing so far has just been adjusting to baseline, removing blanks and trying to identify peaks for dereplication, so that'll be useful. I'll take another look at using MZmine over XCMS Online.
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