A biological question and a balanced (orthogonal) design: the ingredients to efficiently analyze two-color microarrays with Confirmatory Factor Analysis

Table 1 Overview of the balanced reference design*

Hybridization design	Array	Cy3 (green)	Cy5 (red)
SelfSelf	1	A2780	A2780
Ref-CP70	2	A2780	CP70
Ref-C30	3	A2780	C30
Ref-C200	4	A2780	C200
CP70-Ref	5	CP70	A2780
C30-Ref	6	C30	A2780
C200-Ref	7	C200	A2780

* This design was used for the 3 independent RNA isolations from the ovarian cancer cell lines A2780, CP70, C30 and C200 (3 independent cell cultures). In addition one extra 'SelfSelf' was performed in the second replication of the design, resulting in a total of 22 hybridizations.

ISSN: 1471-2164