


Dear R users,

 

 

I would like to
compare chemical profiles of 2 different plant species. My data set consists of
relative proportions of all the compounds in the chemical profile and are
organized in:

- Rows: samples
of 2 species with 15 replicates for species 1 and 6 for species 2

- Columns: 60
compounds 

 

For this kind
of analysis I usually first use the function metaMDS (vegan) to run NMDS with Bray-curtis
distance index with the transformation option (to increase the weight of the
minor compounds). 

Then I transform
my data with the same transformation used in the metaMDS and use adonis (vegan),
permutational manova, to test if there is a significant difference between the
2 species. And finally, if the difference is significant, I use indval (labdsv), Dufrene-Legendre Indicator
Species Analysis, to see which compounds are the most representatives of the chemical
profile of each species.

 

Regarding this dataset, with unbalanced data, I´m a
bit worried that indval does not handle it very well. So I use the function
sample to extract randomly 6 samples from species 1 and run the analysis again
with the species 2, so I have the same number of repetition per group. I did
that 10 times.

 

I have several questions:

Do you think the tests are appropriate for what I
want to do?

Regarding the re-sampling and analysis following,
how should I interpret the results? I only take the compounds that have been
significant more than half of the time? Or just put all the compounds with the
percentage of time they have been significant?

 

In my field people are not so familiar with this
type of analysis so I´m not so sure about my results.

 

I will really really appreciate any help!!!!

 

Thanks a lot!

 

Magali





Magali Proffit, PhD Division of Plant Protection BiologyChemical EcologySwedish University of Agricultural SciencesP.O. Box 102SE-230 53 ALNARPSWEDENtel: +46 (0)40 41 52 49fax: +46 (0)40 46 19 91email: Magali.Proffit@ltj.slu.se, proffitm@gmail.com 		 	   		  
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