I am trying to do microarray analysis on a time-series (5 time points) gene expression (GE) data of 3000 genes. i want to calculate all Vs all (3000 Vs 3000 genes') Pearson correlation coefficient values. I searched a lot in literature and found that some studies normalize the data taking ratios of GE intensity values of individual genes and then Log transform these values, while other studies subtract the control GE intensity value of a gene from the test value. Please guide me on what is the appropriate way of normalisation that would suit my need.
Thanking you in anticipation,