[BioC] limma design question
oriolebaltimore at gmail.com
Sat Nov 22 00:29:42 CET 2008
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.
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.
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