[BioC] Limma: combining 2 microarray studies

J.delasHeras at ed.ac.uk J.delasHeras at ed.ac.uk
Fri Apr 7 18:18:10 CEST 2006

Quoting Ana Conesa <aconesa at ivia.es>:

> Hi,
> I have been asked to analyze jointly two different microarray studies (2
> color technology). They use the same microarray platform and represent the
> same biological process but each one follows a different experimental design
> and evaluate slightly different conditions
> One study has a reference design, while the other is a dye-swap of pairs
> treatment vs. control, schematically
> Study A:
> 	Cy3	Cy5
> chipA1  trt1	reference
> chipA2  trt1	reference
> chipA3  trt2	reference
> chipA4  trt2	reference
> .....
> Study B
> 	  Cy3		Cy5
> chipB1  trt3		control.trt3
> chipB2  control.trt3	trt3
> chipB3  trt4		control.trt4
> chipB4  control.trt3	trt4
> .....
> We would like to make comparisons between treatments in Study A and
> treatments in Study B. (e.g., trt1 and trt3)
> I am not sure on how I should set design and contrasts in Limma to address
> such comparisons (if possible). Maybe someone in the List can give me some
> hints?
> Thank you
> Ana

Hola Ana,

I am not the most experienced here exactly, but what you are trying to 
do sounds a lot like an example in the Limma user's guide: Chapter 17, 
separate channel analysis of two-color data. Have you looked at that?


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

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