[adegenet-forum] Reagarding sPCA: retained scores

[Roy Francis Mathew]

Hi,
I have a question regarding sPCA scores.
While performing an sPCA, the scores to be retained can be retained automatically (scannf=F) or interactively.
How does it decide how many to retain? And if I retain 1 or 3 or 6. I can still plot out just 1 or 2.
Is there any reason why only a few are retained? Why not just retain everything by default? Does this affect any downstream analysis?
Thanks,
Roy