[BioC] limma design question

[Adrian Johnson]

dear group,

I am sorry to ask again design related question. the data is from SMD.
three or two different samples have been obtained from single patient.
Say :
from patient 1 -  (A). a normal tissue, (B). inflamed tissue and (C).
cancer tissue was extracted
from Patient 2 -  (A). a normal tissue (B). cancer tissue was only
extracted and like wise.
A universal reference sample was used to hybridize on Green channel.

This is a paired design and a reference design. Limma manual describes
examples unique to one specific design.
I do not know how to combine two different designs.

My targets file:

FileName	Cy3	Cy5	SibShip (patient)
61453.xls	Ref	B	12
61454.xls	Ref	ACA	12
61459.xls	Ref	N	15
61460.xls	Ref	ACA	15
61461.xls	Ref	N	16
61462.xls	Ref	ACA	16
61463.xls	Ref	N	17
61464.xls	Ref	B	17
61465.xls	Ref	ACA	17



I want to identify BvsN, ACAvsN, ACAvsB.

how could I get design matrix for this type of design.

This is one of those studies where rare cancers have been studied (in 2003).
Unfortunately, this is public dataset (Published in Oncogene) where
experiments have been done using stanford microarray database.

thank you in advance.

Adrian.