We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes. Our goal would be to be able to compare relative gene expression for genes over the different cell lines.
The method we have thought of so far involves calculating some sort of gene-based average (the expression of a particular gene over all the lines) and normalizing our expression data, grouped per gene, based on that. However, we are not sure that this is a valid method for obtaining relative expression data from our data set, especially so that we can compare the data from several lines.
Does this seem like a valid strategy? How is this normalization commonly done? Should we do something differently to get a better comparison?
Thanks so much!