[R] AMOVA error: 'bin' must be numeric or a factor

[Ben Bolker]

Hanne Ballestad <hanne.ballestad <at> bio.uio.no> writes:

>  I am trying to analyse my data using amova 
>  (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova):
> 
>  My input to R is a DNA sequence file, format=fasta
>  	dna<- read.dna("XX.fasta", format="fasta") #left other options as 
>  default
>  	d<- dist.dna(dna, model="raw")
>  	g<- read.table("XXX.design")
> 
>  Load necessary libraries:
>  	library(pegas)

  [snip]

>  Running Amova:
>  amova(d ~ g, nperm = 100)
>  Error in FUN(X[[1L]], ...) : 'bin' must be numeric or a factor
> 
>  How can I solve this "bin" problem?

  [snip]

>  My input file for g looks like this:
> 
>  sequenceA	1
>  sequenceB	1
>  sequenceC	1

 [snip]
> 

  I think the "proper manual" you're looking for is actually the
introductory R material -- try looking at the Introduction to R
that comes with R.  You can look up specific commands such as
"c" and "rep" by using ?c or ?rep .

I'm not sure of the structure of your
data, but I think you probably want g[[2]] (i.e. the second
column of g) as your predictor variable. 

  You might get more specific help on the bioconductor mailing
list.