Valid comparison of gene expression between several genes in several cell lines
This is not an easy task, as there are many factors which you have to take in account. First there are intra-essay differences as slightly different conditions for each set of probes for the repetitions. Then, there are inter-assay differences, as differences in the array slides and so on, this paper ("Analysis of microarray gene expression data") goes into more details.

This articles might be helpful as well:


Multiple-laboratory comparison of microarray platforms
Increasing consistency of disease biomarker prediction across
datasets.
The curse of normalization.
Microarray probe expression measures, data normalization and
statistical validation.


What you could also do is go over the Researchgate, I think there are more people around with a lot of experience in this field.