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?
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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.