[R] Anova

[Ramon Diaz]

Dear Luis,

You might want to take a look at the multtest and genefilter packages (which 
are part of Bioconductor ---www.bioconductor.org---; links to it also from 
R's web page).

Note, however, that no explicit loop would be necessary anyway, since you can 
use, say, 

apply(my.data, 1, my.anova.function)

asuming your data are in a data frame "my.data", where genes are in rows, and 
your "my.anova.function" returns whichever component from an aov or 
summary(aov) you are interested in.

Hope this helps.

Ramón


On Thursday 12 December 2002 19:45, Luis Silva wrote:
> Hi,
>
> I have a microarray matrix 3000x70 for example (genes x
> experiments). This data has more than 2 classes. I would like
> to make some filtering on the genes. For example, I would like
> to exclude genes with the same mean expression across all
> classes. This is a problem of ANOVA
>
> H0:mu1=mu2=...=muk
> H1: at least one is different
>
> First question: Do you think Anova is reasonable for this?
> Second question. How can I do this with R?
> Clearly, I'll have to make some loop to apply this operation to
> all the genes.
>
> Thanks
>
> Luis

-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
http://bioinfo.cnio.es/~rdiaz