Sorry, I send the last email unfinished. I'll restart.

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. Can you tell me if my vector is correct based on my
targets.txt file?


SlideNumber Name FileName Cy3 Cy5 Date
0872 N1 Controle_Cy3x4horas_Cy5_RepI_05Fev2009.gpr WT_RepI 4horas_RepI
05/Fev/2009
0873 N2 4horas_Cy3XControle_Cy5_RepI_05Fev2009.gpr 4horas_RepI WT_RepI
05/Fev/2009
0877 N3 Controle_Cy3X4horas_Cy5_RepII_29Jan2009.gpr WT_RepII 4horas_RepII
29/Jan/2009
0880 N4 4horas_Cy5XControle_Cy3_RepII_29Jan2009.gpr 4horas_RepII WT_RepII
29/Jan/2009
0871 N5 Controle_Cy3X24horas_Cy5_RepI_06Fev2009.gpr WT_RepI 24horas_RepI
06/Fev/2009
0876 N6 24horas_Cy3XControle_Cy5_RepI_06Fev2009.gpr 24horas_RepI WT_RepI
06/Fev/2009
0868 N7 Controle_Cy3X24horas_Cy5_RepII_12Fev2009.gpr WT_RepII 24horas_RepII
12/Fev/2009
0869 N8 24horas_Cy3XControle_Cy5_RepII_12Fev2009.gpr 24horas_RepII WT_RepII
12/Fev/2009

design <- c(1, -1, 2, -2, 1, -1, 2, -2)?

I'm sorry for all those questions, but I'm completely by myself here!

Thanks!

Priscila









On Wed, Feb 18, 2009 at 8:24 AM, Priscila Grynberg <priscilag@gmail.com>wrote:

> 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
>
>


-- 
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]]

