[BioC] Using Anova for microarray data

[James W. MacDonald]

Hi Konika,

As Sean already mentioned, you might want to look at the limma package. 
It seems you have not done so, in which case I will also advise you to 
to do so.

In particular, you should look at the limma User's Guide.

Best,

Jim

On 3/23/2012 10:15 AM, konika chawla wrote:
> 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 at bio.ntnu.no
>> <mailto:chawla at 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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>>
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>
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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