[BioC] LIMMA: analysis of direct design....

[Jakob Hedegaard]

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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