Hi
I tried using the code below for the data design I have
aof <- function(x) {
   m<-data.frame(time, treatmentA, treatmentB, x);
   anova(aov(x ~ time + treatmentA + treatmentB + time * treatmentA * 
treatmentB, m))
}
time <- factor(c(1,1,1,2,2,2,1,1,1,2,2,2,1,1,1,2,2,2))
  treatmentA<-factor(c(1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0)) #control
treatmentB<-factor(c(0,0,1,0,0,1,0,0,1,0,0,1,0,0,1,0,0,1)) #infected
anovaresults <- apply(val, 1, aof)

could you check if it is the correct way to put factors , based on the 
design mentioned previously.
Also, It gives a huge file for each gene and the Fvalues and Pvalues.
Wondering how to write the result in order to get P values for effect of 
treatmentB , or for checking if treatment A and B are same of different.
Could you help
Thanks
Konika

On 03/23/2012 01:55 PM, Sean Davis wrote:
>
> Take a look at the limma package.
>
> On Mar 23, 2012 8:31 AM, "konika chawla" <chawla@bio.ntnu.no 
> <mailto:chawla@bio.ntnu.no>> wrote:
>
>     Hi
>     I need help for using two way anova for microarray data.
>
>     In the 18 data files, have two time points and 3 treatments,and three
>     replicates.
>     Design looks like this
>
>     Timepoint       4       5       4       5       4       5
>     treatment
>
>
>
>
>
>     control         1       4       7       10      13      16
>     Mock    2       5       8       11      14      17
>     infected        3       6       9       12      15      18
>
>
>     Can you suggest how can I do two way ANOVA , time with control and
>     mock
>     and
>     2)  time with control and infected
>
>     Thanks
>     Konika
>
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