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<p>Data were processed using the Microarray Suite 5 (<a class="normal" href="www.affymetrix.com/support/technical/whitepapers/sadd_whitepaper.pdf">MAS 5</a>) protocol of Affymetrix. To simplify comparison between transforms, MAS 5 values of each array were log2 transformed and adjusted to an average of 8 units. In general, MAS 5 data do not perform as well as RMA or PDNN transforms.</p>
<p>Data were processed using the Position-Dependent Nearest Neighbor (<a class="normal" href="http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/" target="_blank">PDNN</a>) method developed by Zhang and colleagues (<a class="normal" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12794640" target="_blank">2003</a>. To simplify comparison between transforms, PDNN values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with careful consideration to balancing samples by sex, age, and environment.</p>
<p>Data were processed using the <a class="normal" href="http://stat-www.berkeley.edu/users/bolstad/RMAExpress/RMAExpress.html" target="_blank">RMA</a> protocol and are presented with secondary normalization to an average expression value of 8 units. To simplify comparison between transforms, RMA values of each array were adjusted to an average of 8 units and a variance of 2 units. This data set was run as a single large batch with effort to balance samples by sex, age, and environment.</p>
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