On Wed, Mar 25, 2009 at 4:07 AM, Mohamed lajnef <lajnef@gmail.com> wrote:

> Hi Sean & Wei
>
> I forgot to tell you that the database is normalized using beadarray
> package, but i am looking for an appropriate methode (limma,anova or...???)
> to extract  the genes differentially expressed by treatment
>

Limma is a fine choice, yes.  The limma user guide and help pages are the
place to start.

Sean



>
> Mohamed
>
> 2009/3/25 Sean Davis <seandavi@gmail.com>
>
>>
>>
>> On Tue, Mar 24, 2009 at 7:06 PM, Mohamed lajnef <lajnef@gmail.com> wrote:
>>
>>> Dear All,
>>>
>>> I have data from illumina  experiments (one colora data) (48803 rows, 120
>>> colones (40 colones for each  treatment) ) and I am looking for the genes
>>> differentially expressed by treatment
>>>
>>> could you tell me please, if i can use the package limma to apply the
>>> differential expression methods (lmFit,eBayes and topGene) or other
>>> method
>>> appropriate to my data ( for instance ANOVA)?
>>>
>>
>> Yes.  You might want to look at the lumi or beadarray packages, as well.
>>
>> Sean
>>
>>
>>
>

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