[adegenet-forum] xvalDapc

[Mark Coulson]

Hi,

I'm running the xvalDapc function for a dataset and wondering how to modify the number of PCA axes retained?

When I run the following
xval1 <- xvalDapc(FD_t, group, n.pca.max=40, result="groupMean", center=TRUE, scale=FALSE, xval.plot=TRUE)

I get results back at 5, 10, 15, 20, 25, 30, 35

However, when I run (on the same dataset)

xval1a <- xvalDapc(FD_t, group, n.pca.max=40, result="groupMean", training.set=0.7, center=TRUE, scale=FALSE, xval.plot=TRUE)

I get results back at 13 different PCA axes levels, roughly by increments of 2


Also, I am looking to specify the increments so tried something like the following:
xval2 <- xvalDapc(FD_t, group, n.pca.max=40, result="groupMean", training.set=0.7, center=TRUE, scale=FALSE, n.pca=seq(5, by=5,to=40),xval.plot=TRUE)

but I don't get these exact increments.

So what determines the scale of the x-axis?

Thanks,
Mark
Inverness College UHI, a partner in the University of the Highlands and Islands www.inverness.uhi.ac.uk Board of Management of Inverness College (known as Inverness College UHI), Scottish Charity No SC021197.
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