[BioC] Timecourse package

[Yu Chuan Tai]

I'd suggest that you look at the help file and the example codes in the 
help file first to see how to use mb.long(). Type

help(mb.long)

Best,
Yu Chuan

On Wed, 18 Feb 2009, Priscila Grynberg wrote:

> 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 at 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 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]]
>>>>>>
>>>>>>
>>>>>>
>>>>>>  _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at 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
>