PCA analysis

[MRS]

Hi everybody,
somebody knows how to manage a large group of related individuals (F2 population) in PCA analysis? I have a database, including parental lines of the F2 population.
I have added 140 individuals (F2) in one step. I got a plotting where all the F2 lines are grouped outside of database line.
Is it strange?
Is it the right way to analyse population like that, if not what is the best way?
Thanks for any hint

[blcr11]

I haven't done much principle component analysis, but the only thing I can think of is that maybe you didn't normalize disparate units, or didn't do it correctly?? 140 observations doesn't strike me as an overly large group, either, but I doubt that has anything to do with anything. Sorry. Not much help I'm afraid.

[MRS]

Thanks for your suggestion. But probably this is not my problem. My data are score (0,1) of AFLP analysis and thethey don't have disparate units. I agree that 140 observations are not a large group, but probably when they are strongly related each other it can interfere, I don't know how, with the analysis. Thank again