Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations

Background: Microarrays measure the binding of nucleotide sequences to a set of sequence specific probes. This information is combined with annotation specifying the relationship between probes and targets and used to make inferences about transcript- and, ultimately, gene expression. In some situations, a probe is capable of hybridizing to more than one transcript, in others, multiple probes can target a single sequence. These 'multiply targeted' probes can result in nonindependence between measured expression levels. Results: An analysis of these relationships for Affymetrix arrays considered both the extent and influence of exact matches between probe and transcript sequences. For the popular HGU133A array, approximately half of the probesets were found to interact in this way. Both real and simulated expression datasets were used to examine how these effects influenced the expression signal. It was found not only to lead to increased signal strength for the affected prob...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Michal J. Okoniewski, Crispin J. Miller
• Keywords: BMCBI 2006, Gene Expression, Sequence Specific Probes, Simulated Expression Datasets