Hi Yu,

I get it. I believe I still don't know how to creat the input file. Just
like the example in the pdf file? Can it read .gpr files?
Priscila

On Wed, Feb 18, 2009 at 3:22 PM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote:

> Hi Priscila,
>
> For limma, I believe there are many experts here who can answer your
> questions.
> By "flip the log2 ratio for Control X T so that you get two replicated
> vectors of log2 ratios", I mean you take the minus of log2 ratios (i.e.
> log2(C/T) becomes -log2(C/T)=log2(T/C)) for those Control X T experiments so
> that all the log2 ratios are treatment to control.
> Then you can use the two vectors of log2 ratios of treatment to control and
> apply mb.long() for picking up differentially expressed genes.
>
> Best,
> Yu Chuan
>
>  On Tue, 17 Feb 2009, Yu Chuan Tai wrote:
>
>  Hi Priscila,
>>
>> Am I right that your data have 2 time points, each with a pair of dye-swap
>> experiments? For each biological replicate, was it sampled repeatedly over
>> time? Looks like timecourse can be used, as long as it's of longitudinal
>> design. You can just flip the log2 ratio for Control X T so that you get two
>> replicated vectors of log2 ratios.
>>
>> Best,
>> Yu Chuan
>>
>> On Tue, 17 Feb 2009, Priscila Grynberg wrote:
>>
>>  Dear BioCs,
>>> I'd like to know if it's possible to analyse two-channel microarray data
>>> using the timecourse package. I read the pdf, and the examples use Affy
>>> data.
>>>
>>> I'm working with 70-mer oligonucleotide microarray slides. Here is my
>>> experimental design:
>>>
>>> Control X T1 (Biological Replicate 1)
>>> T1 X Control (Biological Replicate 1)
>>>
>>> Control X T1 (Biological Replicate 2)
>>> T1 X Control (Biological Replicate 2)
>>>
>>> Control X T2 (Biological Replicate 1)
>>> T2 X Control (Biological Replicate 1)
>>>
>>> Control X T2 (Biological Replicate 2)
>>> T2 X Control (Biological Replicate 2)
>>>
>>> My control sample is really important for my analysis.
>>>
>>>
>>> --
>>> Priscila Grynberg, B.Sc., M.Sc.
>>> Doutoranda em Bioinform??ica (Bioinformatics D.Sc student)
>>> Laborat??io de Gen??ica Bioqu??ica
>>> Universidade Federal de Minas Gerais
>>> Tel: +55 31 3409-2628
>>> CV: http://lattes.cnpq.br/8808643075395963
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>>
>>>
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>>
>


-- 
Priscila Grynberg, B.Sc., M.Sc.
Doutoranda em Bioinformática (Bioinformatics D.Sc student)
Laboratório de Genética Bioquímica
Universidade Federal de Minas Gerais
Tel: +55 31 3409-2628
CV: http://lattes.cnpq.br/8808643075395963

	[[alternative HTML version deleted]]

