Dear Yu and BioCs,

Yes, I have a longitudinal time course experiment, with 2 independent
biological replicates. Each one had their samples extracted in different
months, but they were made exactly like the other: 4hs and 24 hs after
treatment. I have also two more times to analyse, but for previously
results, I'll analyse just the first 2 times.

I'm not very good in statistics! I don't know how how to "flip the log2
ratio for Control X T so that you get two replicated vectors of log2
ratios". I'll tell what I have done so far:

1) I used limma and marray to check the quality of the data and to normalize
using robustspline method (the best for my data - I tried all of them). Can
I use those results as the input for Timecourse package?

2) I believe that I must create a vector to explain my design experiment for
limma package. I


On Wed, Feb 18, 2009 at 3:42 AM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>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]]
>>
>>
>>


-- 
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

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