[BioC] Timecourse package

[Yu Chuan Tai]

I see. Timecourse doesn't deal with inter-replicate correlations. In that 
case, you have to assume A_01 and A_02 are independent and 
you have 4 replicate vectors. Or you can average A_01 and A_02
(after you flip the log ratios of one of them) and you have 2 replicate 
vectors. Alternatively, you may also consider 
using limma package, which has a function for dealing with inter-replicate 
correlations. If you decide to continue with Timecourse, the analysis will 
be in the same way as Affy, and you can just follow the example codes in 
the help file.

Best,
Yu Chuan

  On Wed, 18 Feb 2009, Priscila Grynberg wrote:

> I already read everything. I understand the arguments in the examples,
> because it's Affy data. But for two-channel oligo microarray, with dye-swap,
> it doesn't fit. That's why I need some help.
> I have 4 slides for each time. But I can't call them A_01, A_02, A_03, A_04
> and B_01, B_02, B_03, B_04, because A_01 and A_02 are the dye-swap. They are
> not independent samples. How can I explain this to the algorithm? I'm a
> biologist. It's hard to me. But I'll keep trying.
>
> Thanks,
>
> Priscila
>