I get it! Now I'm in trouble with mb.long arguments. Would you mind to help
me?
Just remembering my design:

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_Cy3XControle_Cy5_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



object - OK
method - 1D, paired or 2D? I would go for "2D", but maybe is a "paired".
type - default
times - 2? (Ref X 4hs and Ref X 24hs)
reps - I have 2 biological replicates, but I don't think this is what "reps"
wants.
prior.df - default
prior.COV - default
prior.eta - default
condition.grp - I dpn't know this one
rep.grp - This one I need. But how?
time.grp - This one I need. But how?
one.sample - false?
ref - I still don't know!
p - default
out.t - I'd like to be true
tuning - default
HotellingT2.only - True


Thanks so much!

Priscila


On Wed, Feb 18, 2009 at 3:38 PM, Yu Chuan Tai <yuchuan@stat.berkeley.edu>wrote:

> No, it doesn't take gpr files. As indicated in the help file, it takes
> "An object of class matrix, MAList, marrayNorm, or exprSet containing
> log-ratios or log-values of expression for a series of microarrays"
>
> These are objects you get after you pre-process your raw data. Best,
> Yu Chuan
>
>
> On Wed, 18 Feb 2009, Priscila Grynberg wrote:
>
>  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]]
>>>>>
>>>>>
>>>>>
>>>>>  _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor@stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>>
>>
>> --
>> 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

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