I have a table with mass spectrometry data from some morphospecies of plants, using different techniques.
sp technique mz abundance sp1 ESIneg 118.89 3.01 sp1 ESIneg 172.72 3.20 sp1 ESIneg 202.94 3.80 sp1 ESIpos 118.30 2.59 sp1 ESIpos 170.68 3.13 sp1 ESIpos 257.97 3.28 sp2 ESIneg 132.33 22.22 sp2 ESIneg 211.84 3.87
I want to use some sort of cluster analysis to test if these species are the same or different. I've been reading different papers, but they don't show their data table, only the sort of analysis done (Kmeans, Ward, Model based...), most times in proprietary software.
Most tutorials about cluster analysis start with a XY table, which is not the case here.
I want to do it in R, I know there are LOTS of packages available, so maybe someone could point me to a more didactic paper or tutorial, or perhaps a specific package/function? And is it possible to use all different techniques at once, or will I have to analyze each one separately?