[BioC] limma design matrix question

[Marcelo Luiz de Laia]

Hi All,

I have this targets:

> ka.rest.targets
  SlideNumber          FileNames      Cy3     Cy5
1           1 Ka_Rest_Rep_1.datr Control Treated
2           2 Ka_Rest_Rep_2.datr Control Treated
3           3 Ka_Rest_Rep_3.datr Control Treated

and I proceed

> design <- designMatrix(ka.rest.targets,ref="Control")
> design
  Treated
1       1
2       1
3       1
> ?designMatrix

Is this correct??

I am confused because I read this in help:

"There is a need for design matrices for direct two-color design
 and for single-channel experiments but, this version is only for
 reference designs."
"Examples:
  targets <-
data.frame(Cy3=c("Ref","Control","Ref","Treatment"),Cy5=c("Control","Ref","T
reatment","Ref"))
  designMatrix(targets, "Ref")"

In my case, "REF" is my control (Control)?

I don't understand the difference between the Reference and Control!

Thanks

Marcelo Luiz de Laia, M.Sc.
Dep. de Tecnologia, Lab. Bioquímica e de Biologia Molecular
Universidade Estadual Paulista - UNESP
Via de Acesso Prof. Paulo Donato Castelane, Km 05
14.884-900 - Jaboticabal, SP, Brazil
PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.)
Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia at yahoo.com
---