[adegenet-forum] double-zero problem in genetic data

Xavier Turon xturon at ceab.csic.es
Thu Feb 10 16:53:02 CET 2011


I'm new in this forum and I have just done my first DAPC analyses. I 
have a question, and sorry if it is naive or has already been discussed 
at previous times.

Coming from the field of ecology, I am reluctant to analyse matrices 
with many zeroes with PCA. This is typical of matrices of species 
abundance, where absence of a species in two localities (double-zeros) 
does not mean at all that both localities are related. Many double 
absences can result in spurious high covariances.

I wonder if the same cannot be said of the individuals * alleles 
matrices, which by their very nature have plenty of zeros (i.e., the 
absence of a given allele in two individuals can be interpreted as 
indicating similarity between them?)

Thanks for your inputs on this matter,


Xavier Turon
Dept. of Marine Ecology
Center for Advanced Studies of Blanes (CEAB, CSIC)
Accés a la Cala S. Francesc 14
17300 Blanes (Girona)

E-mail: xturon at ceab.csic.es
Phone: +34 972 336101
Fax: +34 972 337806

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