[BioC] Using Anova for microarray data
James W. MacDonald
jmacdon at uw.edu
Mon Mar 26 15:57:41 CEST 2012
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
>>
>> [[alternative HTML version deleted]]
>>
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>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099
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