There are many sources of variation in dual labelled microarray experiments, including data acquisition and image processing. The final interpretation of experiments strongly relies on the accuracy of the measurement of the signal intensity. For low intensity spots in particular, accurately estimating gene expression variations remains a challenge as signal measurement is, in this case, highly subject to fluctuations.
Glatigny, A., Delacroix, H., Tang, T., François, N., Aggerbeck, L., & Mucchielli-Giorgi, M. H. (2009). Characterisation and correction of signal fluctuations in successive acquisitions of microarray images. BMC Bioinformatics, 10. https://doi.org/10.1186/1471-2105-10-98