Direct calibration of P<smcaps>ICKY</smcaps>-designed microarrays
2009
Ronald Pamela C | Hsing Yue-Ie C | Park Sunyoung | Trisiriroj Arunee | Chou Hui-Hsien | Schnable Patrick S
Abstract Background Few microarrays have been quantitatively calibrated to identify optimal hybridization conditions because it is difficult to precisely determine the hybridization characteristics of a microarray using biologically variable cDNA samples. Results Using synthesized samples with known concentrations of specific oligonucleotides, a series of microarray experiments was conducted to evaluate microarrays designed by P<smcaps>ICKY</smcaps>, an oligo microarray design software tool, and to test a direct microarray calibration method based on the P<smcaps>ICKY</smcaps>-predicted, thermodynamically closest nontarget information. The complete set of microarray experiment results is archived in the GEO database with series accession number GSE14717. Additional data files and Perl programs described in this paper can be obtained from the website <url>http://www.complex.iastate.edu</url> under the P<smcaps>ICKY</smcaps> Download area. Conclusion P<smcaps>ICKY</smcaps>-designed microarray probes are highly reliable over a wide range of hybridization temperatures and sample concentrations. The microarray calibration method reported here allows researchers to experimentally optimize their hybridization conditions. Because this method is straightforward, uses existing microarrays and relatively inexpensive synthesized samples, it can be used by any lab that uses microarrays designed by P<smcaps>ICKY</smcaps>. In addition, other microarrays can be reanalyzed by P<smcaps>ICKY</smcaps> to obtain the thermodynamically closest nontarget information for calibration.
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