Standard experiment/project design:
Each microarray experiment that we perform is divided into 'replica groups' that correspond to each sample-control pairing. We recommend that each sample and control be an indepdendent biological preparation. This ensures that we can average accross independent biological replicates and therefore enhances data quality.
Experiment organisation
We shall extract RNA from each of your biological samples, label and then hybridise them to four microarray slides. Two of the four slides will be 'dye-swaps', meaning that the sample that was labelled with Cy3 is now labelled with Cy5, and vise versa. This is to accommodate for the differential labelling efficiencies of each dye. This too will enhance data quality.
