[adegenet-forum] sPCA screeplot

Moussy, Caroline cm323 at exeter.ac.uk
Mon Jun 25 21:19:05 CEST 2012

Dear all,

My dataset consists of 699 individuals sampled at 36 locations (colonies) and genotyped at 10 microsatellites. I have uploaded my dataset in a STRUCTURE format and performed a DAPC analysis on the genind object.
I wanted to compare these results with results from a sPCA on the genpop object using Delauney triangulation as connection network.
When calling for the spca plot, the connection network, 3 x score 1 and eigenvalues plots are displayed but the spatial and variance components of the eigenvalues plot doesn't appear.

When calling for it separately using screeplot, it doesn't come up either.
I get the following error message:
Error in apply(X, 2, f1) : object 'X' not found

The same message appears when calling for the summary of the spca.

> delauney<-spca(pop,ask=F,type=1,scannf=F,nfposi=2,nfnega=0) #select 2 axes for positive, 0 negative

> plot(delauney)

Error in apply(X, 2, f1) : object 'X' not found

> screeplot(delauney)

Error in apply(X, 2, f1) : object 'X' not found

> summary(delauney)

Spatial principal component analysis

Call: spca(obj = pop, scannf = F, nfposi = 2, nfnega = 0, type = 1,

    ask = F)

Error in apply(X, 2, f1) : object 'X' not found

The same issue occurs when I used other connection networks.

I am at loss trying to figure out what went wrong and how I could obtain the screeplot. Would anyone be able to help?

Thanks a lot.


Caroline Moussy
PhD Spatial ecology of the serotine bat

Centre for Ecology and Conservation
University of Exeter
Tremough campus
TR10 9EZ

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