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BMCBI
2005

Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in

9 years 3 months ago
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in
Background: Comparison of data produced on different microarray platforms often shows surprising discordance. It is not clear whether this discrepancy is caused by noisy data or by improper probe matching between platforms. We investigated whether the significant level of inconsistency between results produced by alternative gene expression microarray platforms could be reduced by stringent sequence matching of microarray probes. We mapped the short oligo probes of the Affymetrix platform onto cDNA clones of the Stanford microarray platform. Affymetrix probes were reassigned to redefined probe sets if they mapped to the same cDNA clone sequence, regardless of the original manufacturer-defined grouping. The NCI-60 gene expression profiles produced by Affymetrix HuFL platform were recalculated using these redefined probe sets and compared to previously published cDNA measurements of the same panel of RNA samples. Results: The redefined probe sets displayed a substantially higher level o...
Scott L. Carter, Aron C. Eklund, Brigham H. Mecham
Added 15 Dec 2010
Updated 15 Dec 2010
Type Journal
Year 2005
Where BMCBI
Authors Scott L. Carter, Aron C. Eklund, Brigham H. Mecham, Isaac S. Kohane, Zoltan Szallasi
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