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Topic: Metabolite PLS-DA analysis bad p-value (Read 2562 times) previous topic - next topic

Metabolite PLS-DA analysis bad p-value

Hi All,

I'm doing some metabolomics analysis using the web based tool available from http://www.metaboanalyst.ca/. I'm using a concentration table as input.

For the PLS-DA analysis my samples 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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Thanks

Re: Metabolite PLS-DA analysis bad p-value

Reply #1
Hi august,

I don't have the first hand knowledge on PLS-DA to comment on your question,
but I remember the excellent keynote by Rasmus Bro at Metabolomics 2012
( http://www.metabolomics2012.org/keynote-speakers/ ) where he used
Matlab (his favourite tool, but can probably done in R as well) to draw
a fully RANDOM dataset, a fully RANDOM Y and got a (visually) nice separation
of the classes.

Maybe this Metabolomics journal article can also help ?
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337399/

Yours,
Steffen

P.S. : If you succeed to reproduce Rasmus' PLS-DA on random data in R,
I'd love to see a code example posted here...
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE