Power-law Signatures and Patchiness in Genechip Oligonucleotide Microarrays

TL;DR

This study examines the distributional patterns and local correlation structures of probe intensities in Genechip microarrays, revealing fundamental concerns about data interpretation due to observed similarities and patchiness.

Contribution

It uncovers qualitative similarities and patchiness in probe intensities, challenging current assumptions in microarray data analysis.

Findings

Similar distributional signatures in PM and MM probes across labs

Persistent patchiness in raw and background-subtracted data

Raises concerns about microarray data interpretation

Abstract

. Genechip oligonucleotide microarrays have been used widely for transcriptional profiling of a large number of genes in a given paradigm. Gene expression estimation precedes biological inference and is given as a complex combination of atomic entities on the array called probes. These probe intensities are further classified into perfect-match (PM) and mis-match (MM) probes. While former is a measure of specific binding, the lat-ter is a measure of non-specific binding. The behavior of the MM probes has especially proven to be elusive. The present study investigates qualita-tive similarities in the distributional signatures and local correlation struc-tures/patchiness between the PM and MM probe intensities. These qualita-tive similarities are established on publicly available microarrays generated across laboratories investigating the same paradigm. Persistence of these similarities across raw as well as background subtracted probe intensities is also investigated. The results presented raise fundamental concerns in inter-preting Genechip oligonucleotide microarray data.