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Topic: Galaxy metabolomics workflow (Read 284 times) previous topic - next topic

Galaxy metabolomics workflow

 Hi everyone, I am new to the forum and metabolomics analysis. I am going straight to the point because I'm pretty desperate and hope someone can help me. :'( Please!
I am working with an untargeted UHPLC-MS dataset (plasma samples). After much research, I converted the data from Bruker to netCDF format for xcms analysis in R and Galaxy.
I have considerable doubts:
First, I have more spectra in positive than negative ionization mode. Moreover, the files of negative mode take up more memory and could not be loaded entirely to Galaxy (I tried different compression apps to reduce its dimension). Therefore, I split it into distinct and smaller datasets based on the categories. Finally, every smaller dataset is pre-processed separately(maintaining the same parameter of the treatments for all subsets). Is this considered a correct approach?
Once I obtained the data matrix with extracted ions for positive and negative ions, should they have the same dimension to be processed with a ''Camera.combinexsAnnox''(This function check annotation of ion species with the help of a sample from opposite ion mode.)
Any suggestions?


 

Re: Galaxy metabolomics workflow

Reply #1
Hi katy - which Galaxy instance are you processing your files on?

Second, the positive and negative data can be processed separately.

What exactly do you mean with preprocessing for your files?

I'm not an expert on CAMERA but I think this is the right way.