[adegenet-forum] PCA query?

[AVIK RAY]

Hi all
bit of confusion with PCA in general, I did PCA in adegenet and it has 
shown some plot with multiple clusters. My data is tetraploid 
microsatellite data and I need to find out potential clusters i.e. some 
individuals are more similar than others with allele data. But If not 
mistaken PCA converts allele information into some synthetic variable 
and does clustering where we tend to loose out lot of information since 
it will select most but not all alleles; so in that sense does PCoA/ 
Multidimentional scaling or simply clustering analysis (e.g. K means or 
hierarchical clustering) make more sense?
Thanks in advance for reply

AVIK