R help - Mar 2012 - (no subject)

Hey guys,

if i do a correspondance analysis, e.g.:

table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11,
   8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1",
   "gene2", "gene3", "gene4", "gene5"),
c("codon1", "codon2",
   "codon3")))

Library(ca)

plot(ca(table))

is there a way that i can see the "second principal axis" of this
analysis?

Aoife

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Le lundi 12 mars 2012 ? 14:48 +0000, aoife doherty a ?crit
:
> Hey guys,
> 
> if i do a correspondance analysis, e.g.:
> 
> table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11,
>    8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1",
>    "gene2", "gene3", "gene4",
"gene5"), c("codon1", "codon2",
>    "codon3")))
> 
> Library(ca)
> 
> plot(ca(table))
> 
> is there a way that i can see the "second principal axis" of this
analysis?
You're joking, right? :-p How many dimensions are you able to represent
on a screen? Two, isn't it? So the vertical axis is your second
dimension.

You can get details as this:
summary(ca(table))

Principal inertias (eigenvalues):

 dim    value      %   cum%   scree plot               
 1      0.394553  92.8  92.8  *************************
 2      0.030431   7.2 100.0                           
        -------- -----                                 
 Total: 0.424984 100.0           

Here you see the second axis accounts for only 7.2% of the total
variance.


Cheers