I've been given an old set of microarray data and a task to 'analyse and get whatever possible out of them'. The experimental design was the following:
- two mutant samples + two control samples (so, we have two biological replicates, right?);
- two RNA extractions from each sample;
- hybridization in duplicate;
- two-color microarray, and each channel was scanned separately.
So, what I have after cleaning the data is a matrix 5000 (the number of genes) by 16 (2^4).
What would be an appropriate way to average these data, normalize them and determine differential expression?
Thanks in advance!