Hi! I'm a master's degree student/researcher in a metabolomics group, trying to do a dissertation about a metabolomics analysis of a dataset of cucumber, and it has to be using R. Previously I've used software as SIMCA, but I'm really noob with R... I just know basic things that I learnt in the master, but they didn't focus in the treatment of spectral data or say anything about metabolomics, and I'm reaally lost :'( .
I'm trying to perform a standard metabolomics analysis in R (PCA, PLS), with 1D 1H-NMR data. The corresponding file is in a .xlsx format, and it contains columns with the sample's names, the specie, the ripeness state, and the metabolites. The NMR data has been acquired and proccessed with TopSpin, and the bucketing was performed with Amix (0.04 ppm buckets). I'm gonna atach a file with an extract of the file, so you have a better insight of it.
Well, the problem is that I don't really know which kind of treatment I have to apply to this spectral data before doing the PCA, PLS (etc). I know that I have to somehow clean and normalize data, but I don't really know if there is like a specific package for this kind of NMR data, or with basic R packages I'd be able to do all of this...
Sorry about all this huge text, but I do need help! If you know any tutorial about some kind of similar dataset It would be of help too, I just want to learn how to perform this!
Thank you so much!
Hmmm. I hope you have a supervisor that can help you...
You can find packages here: https://rformassspectrometry.github.io/metaRbolomics-book/0203-R_packages_for_metabolomics-NMR_data_handling_and_pre_processing.html
Some of them probably has some kind of tutorial.