[R] principal component analysis for class variables:somenone has experience with made 4 and plotgenes?

[andreiabb]

Alain Guillet-2 wrote:
> 
> The PCA doesn't work with class variables so the error is normal. You 
> should try to work with a discriminant factorial analysis (see 
> discrimin.coa in ade4).
> 
> Alain thanks for the tip but it did not work, well then I manaege to put
> it to work but the result is very strange. 
> Alain
> 
> However I found a another package made4, a function called plotgenes, this
> is to make a kind of PCA analysis using gene coordenates, so I think it
> can fit well my type of data (now I changed to numerical variables and one
> class variable(popo name) , but I am getting an error message again,
> 
> plotgenes(Df[,1:2], nlab=2, varlabels=breed, boxes=T)
> Error in scatterutil.base(dfxy = dfxy, xax = xax, yax = yax, xlim = xlim, 
> : 
>         unused argument(s) (varlabels = c(4, 2, 2, 4, 4, 2, 2, 2, 2, 3, 3,
> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 2, 2,
> 2, 4, 4, 4, 4, 4, 3, 3, 2, 2, 2, 2, 2, 3, 1, 1, 1, 4, 3, 3, 3, 3, 3, 3, 3,
> 3, 3, 3, 3, 3, 3, 2, 3, 3, 4, 3, 4, 4, 4, 2,
> 
> Thanks 
> Andy
> 
> 
> andreiabb wrote:
>> Dear Forum,
>>
>> I have a class variable 1 (populations A-E), and two other class
>> variables,
>> variable 2 and variable 3. What I want is to see if the combination of
>> var 2
>> and var 3, will give me a pattern that allows to distinguish populations. 
>> I found several packages like ade4, with pcaiv function and factoMineR.
>> but
>> there are not working. Using the ade4 package, when I try to build the
>> pca:
>>  pca1 <- dudi.pca(D, scan = FALSE, nf = 2)
>> Error in v * row.w : non-numeric argument to binary operator
>>
>> Does someone has suggestions? 
>> Thanks,
>> Andy
>>   
> 
> -- 
> Alain Guillet
> Statistician and Computer Scientist
> 
> SMCS - Institut de statistique - Université catholique de Louvain
> Bureau d.316
> Voie du Roman Pays, 20
> B-1348 Louvain-la-Neuve
> Belgium
> 
> tel: +32 10 47 30 50
> 
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