[BioC] Using Anova for microarray data

[Sean Davis]

On Mon, Mar 26, 2012 at 10:54 AM, konika chawla <chawla at bio.ntnu.no> wrote:
> Hi
> Sorry but if you mean
> http://bioconductor.org/packages/2.6/bioc/vignettes/limma/inst/doc/usersguide.pdf
> <http://bioconductor.org/packages/2.6/bioc/vignettes/limma/inst/doc/usersguide.pdf>
> There is nothing about using anova in this document.
> Could you please point me to another document, which explains ANOVA?
> Thanks
> Konika

Hi, Konika.

Limma uses the concept of a linear model.  ANOVA is a subset of this
class of models.  If you use limma on single-channel or
common-reference two-color data, the limma approach is conceptually
equivalent to ANOVA on each gene.  In using limma, you also get the
benefit of pooled variance estimates, important for relatively small
sample sizes typical of microarrays.

Sean



>
> On 03/26/2012 03:57 PM, James W. MacDonald wrote:
>> 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
>>>
>
>
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