Two-Color Array with Sample in One Color and Reference in Another

Question

[Nifaste]

Dear all,

I'm analyzing microarray in which each experimental sample (labeled with Cy5) is hybridized against a common reference sample (labeled with Cy3). Samples were obtained from wild-type and different mutants. For each sample, I have 6 biological replicates. So finally I've 36 experiments.

In a first time, I've to determine the mRNA expression level in wild-type condition (in order to have a liste of mRNA that are expressed).

I'm little confused, I don't know how to proceed.

The data are stored in a RGList where RGList$R are raw data value for wild-type and RGList$G are raw data for the reference.

In a first step I did: normalizeVSN(RGList).

And I wanted to start with the A-value. What do you think about that?

[olle.nordesjo]

If you mention what package you use and show the structure of the data, things might be a lot clearer for people wanting to give an answer.