Expression Analysis Introduces New Technique To Improve Performance Of Affymetrix GeneChip(R)

Durham, NC - Expression Analysis, Inc. has deployed an all-new method of utilizing Affymetrix probe sets when computing signal values on a GeneChip(R). Known as REDI(TM) (REDuction of Invariant Probes) analysis, this new technique essentially removes or masks the affect caused by potentially invariant probes within a probe set in order to provide a more accurate indication of potential differential expression.

"This was an original research project begun in 2003 to address concerns about the affect of some individual oligonucleotide probes," said Dr. Wendell Jones, Expression Analysis Senior Statistician and primary force behind the creation of REDI. "A significant number of probes that appeared to be partially or completely non-responsive are now known to exist, but methods of mitigating them simply were not adequate. We are pleased to be the first organization to provide REDI(TM) as a useful solution to this issue."

Expression Analysis conducted an extensive review of HG-U133-based PM probes using thousands of hybridizations of GeneChips combined with RefSeq-based probe sequence analysis. The study suggested that approximately 30% of the HG-U133A PM probes were non-responsive or relatively invariant, affecting more than 80% of the probe sets. Similar results were subsequently found for Rat and Mouse chips.

In addition, Expression Analysis found that the impact of these probes served to underestimate fold change differences or mask differential expression entirely when probesets contained a large number of these probes. The REDI analysis, however, typically augments a differential gene list by 25% - 200% when the lists are based on significance and fold change thresholds.

According to Expression Analysis Founder and COO, Steve Casey, REDI can be used with any of the current, well-known signal measures such as RMA, PDNN, dChip, MAS5, or PLIER. "We use CEL files with the chosen signal measure algorithm to augment differential gene lists for Human, Rat, and Mouse chips. We look forward to supporting and enhancing the value of Affymetrix experiments with this powerful new bioinformatics tool."

SOURCE: Expression Analysis, Inc.