[adegenet-forum] PCA for microsat data

[Spencer Bruce]

I've done everything in the DAPC tutorial using this data set over and over
no problem, but now I'm attempting to do a simple PCA and I seem to keep
running into problems with my genind object.

I'm sure ill get some backlash for being a self-taught beginner here, but
any help is really greatly appreciated.

I've imported my STRUCTURE file as a Gendind object no problem.
Right off the bat its as if adgenet does not recognize the data in the
object, see object and following code below...

>fish
  #####################
   ### Genind object ###
   #####################
- genotypes of individuals -

S4 class:  genind
@call: read.structure(file = file, missing = missing, quiet = quiet)

@tab:  391 x 172 matrix of genotypes

@ind.names: vector of  391 individual names
@loc.names: vector of  11 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the  172 columns of @tab
@all.names: list of  11 components yielding allele names for each locus
@ploidy:  2
@type:  codom

Optional contents:
@pop:  factor giving the population of each individual
@pop.names:  factor giving the population of each individual

@other: - empty -

> data(fish)
Warning message:
In data(fish) : data set ‘fish’ not found
> sum(is.na(fish$tab))
[1] 166
> X <- scaleGen(fish, NA.method="mean")
Error in .local(x, ...) : unused argument (NA.method = "mean")
> class(X)
Error: object 'X' not found

I also tried this:
> X <- scaleGen(fish$tab, NA.method="mean")
Error in (function (classes, fdef, mtable)  : unable to find an inherited
method for function ‘scaleGen’ for signature ‘"matrix"’

Am i missing something wildly simple here? Any help is greatly greatly
appreciated...
-- 
Spencer A Bruce
113 Hill St.
Troy, NY 12180
518 225 0787
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