[BioC] LIMMA: analysis of direct design....
Jakob Hedegaard
Jakob.Hedegaard at agrsci.dk
Tue Feb 8 17:05:28 CET 2005
Hi!
We have data from an experiment conducted to compare three different
methods (1,2 and 3) for amplifying RNA. RNA from two tissues (A and B)
were amplified with the three different methods and labeled. The same
dye was assigned to the same tissue in all hybridizations (no dye-swap).
Three slides were hybridized within each method.
Slide Method Cy3 Cy5
1 1 A B
2 1 A B
3 1 A B
4 2 A B
5 2 A B
6 2 A B
7 3 A B
8 3 A B
9 3 A B
The data from each slide is background corrected and loess normalized
within each slide followed by quantile normalization between slides.
We want to test whether the three different methods reveal the same
genes to be differentially expressed between tissue A and B - and
whether two of the methods resemble each other more than the third.
How should the design/contrast matrix look like?
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Jakob Hedegaard
Danish Institute of Agricultural Sciences
Department of Genetics and Biotechnology
Molecular Genetics and System Biology
Building K25
Research Centre Foulum
P.O. box 50
DK-8830 Tjele
Denmark
Tel: (+45)89991363
Fax: (+45)89991300
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