[R-sig-genetics] a-score in adegenet

[John S Denton]

Hello,

I am using the a-score to determine the optimal number of PCs to retain in a discriminant function of principal components analysis, and am trying to figure out whether the result I am getting is pathological or not.

I am trying to find the discriminant axes between two groups. One group is much larger than the other. The variances explained by the PCs do not fall off rapidly--the first 58 PCs explain ~95% of the variance.

When I run optim.a.score(), I get a decaying curve without an internal optimum. The function says retaining only a single PC is optimal, with an a-score of ~0.4. I thought this might be an artifact of default values, to I increased the number of PCs at which to conduct simulations (n option) and increased the number of simulations per PC point to 50 (from 10), but I still get the boundary answer of 1 PC.

Is this valid, or might this be a pathology of diffuse PC variation distribution and asymmetric sample sizes?

Thanks!

~John

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