[adegenet-forum] Very different numbers in groups with same paramters using find.clusters

[Markus Ruhsam]

Hello,

I want to do a DAPC on a dataset containing 1548 SNPs starting with the find.clusters command but get wildly different numbers in each group when I repeat the command using exactly the same parameters. Does anybody have an explanation for this?

Thank you

Markus


> grp <- find.clusters(rul, max.n.clust=10)

Choose the number PCs to retain (>=1):

400

Choose the number of clusters (>=2:

3

> table(pop(rul), grp$grp)



               1   2   3

  native       2 131  52

  non-native  67   3   1

  hispanica    5   0   0

  odd         12 113  41



> grp <- find.clusters(rul, max.n.clust=10)

Choose the number PCs to retain (>=1):

400

Choose the number of clusters (>=2:

3

> table(pop(rul), grp$grp)



               1   2   3

  native       1   1 183

  non-native  15  51   5

  hispanica    0   5   0

  odd          0  12 154



> grp <- find.clusters(rul, max.n.clust=10)

Choose the number PCs to retain (>=1):

400

Choose the number of clusters (>=2:

3

> table(pop(rul), grp$grp)



               1   2   3

  native      49 134   2

  non-native   1   3  67

  hispanica    0   0   5

  odd         41 113  12







Dr Markus Ruhsam
Molecular Plant Ecologist
Royal Botanic Garden Edinburgh
20A Inverleith Row
Edinburgh
EH3 5LR
United Kingdom

Tel: +44 (0) 131 248 2859
Fax: +44 (0) 131 248 2901

http://www.rbge.org.uk/science/genetics-and-conservation/markus-ruhsam-homepage

The mission of the Royal Botanic Garden Edinburgh is to "To explore, conserve and explain the world of plants for a better future"


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