I'm doing some metabolomics analysis using the web based tool available from http://www.metaboanalyst.ca/
For the PLS-DA analysis my samples show good separtion, however the permutation p-value is bad. I'm very new to this kind of analysis, and I'm not sure if I'm making some mistakes. Can permutation values be bad if separation between samples are good? Moreover as the PLS-DA model is bad, can I use the metabolites with VIP values >1.0? Or are these VIP values useless as well?
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