[BioC] Timecourse package

[Yu Chuan Tai]

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
>