[BioC] Timecourse package

[Yu Chuan Tai]

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 at 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
>