[BioC] Anova for microarrays

[James W. MacDonald]

You don't want to do things that way. Instead, you want to use either 
limma, multtest, sigggenes, etc. Personally I tend towards limma.

library(BiocInstaller)
biocLite(limma)
library(limma)
limmaUsersGuide()

will get you started.

Best,

Jim



On 12/13/2012 10:39 AM, listas de consultas wrote:
> Hi,
>
> I need help for using one way anova for microarray data.
> In 20 files, I have 5 treatment and 4 replicates for each treatment.
>
> I have the following code:
>
> .
> .
> .
> treatment<- gl(5,4,20, label=c("T1","T2","T3","T4","T5"))
> # define ANOVA function
> aof<- function(x) {
>    m<-data.frame(treatment, x);
>    anova(aov(x ~ treatment, m))
> }
>
> anovaresults<- apply(sdata, 1, aof)
>
>
> Can you suggest how can I do one way ANOVA for 5 treatment and to make
> all the comparations between treatments?
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099