  Affymetrix Genechip microarrays are used widely to determine the simultaneous
expression of genes in a given biological paradigm. Probes on the Genechip
array are atomic entities which by definition are randomly distributed across
the array and in turn govern the gene expression. In the present study, we make
several interesting observations. We show that there is considerable
correlation between the probe intensities across the array which defy the
independence assumption. While the mechanism behind such correlations is
unclear, we show that scaling behavior and the profiles of perfect match (PM)
as well as mismatch (MM) probes are similar and immune to background
subtraction. We believe that the observed correlations are possibly an outcome
of inherent non-stationarities or patchiness in the array devoid of biological
significance. This is demonstrated by inspecting their scaling behavior and
profiles of the PM and MM probe intensities obtained from publicly available
Genechip arrays from three eukaryotic genomes, namely: Drosophila Melanogaster,
Homo Sapiens and Mus musculus across distinct biological paradigms and across
laboratories, with and without background subtraction. The fluctuation
functions were estimated using detrended fluctuation analysis (DFA) with fourth
order polynomial detrending. The results presented in this study provide new
insights into correlation signatures of PM and MM probe intensities and
suggests the choice of DFA as a tool for qualitative assessment of Affymetrix
Genechip microarrays prior to their analysis. A more detailed investigation is
necessary in order to understand the source of these correlations.
