Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots.
Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots.
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DOI：
10.4137/cin.s9055
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发表时间：
2012
影响因子：
2
通讯作者：
Kornblau SM
中科院分区：
文献类型：
--
作者：
Neeley ES;Baggerly KA;Kornblau SM
反相蛋白质阵列 (RPPA) 可同时测量许多样品中蛋白质的相对表达水平。从这些阵列观察到的信号是真实信号、加性背景和乘性空间效应的组合。仅靠背景扣除不足以消除数据中的所有非生物趋势。我们开发了一种表面调整，它使用来自阳性对照点的信息来校正阵列上超出附加背景的空间趋势。该方法使用广义加性模型来估计阳性对照的平滑表面。当以稀释系列打印阳性对照时，嵌套表面调整会执行基于强度的校正。当适用时，表面调整能够消除空间趋势并在载玻片重复一致性内增加，比单独的背景扣除更好，如两组阵列所示。这项工作证明了在阵列上包含阳性对照点的重要性。
Reverse phase protein arrays (RPPA) measure the relative expression levels of a protein in many samples simultaneously. Observed signal from these arrays is a combination of true signal, additive background, and multiplicative spatial effects. Background subtraction alone is not sufficient to remove all nonbiological trends from the data. We developed a surface adjustment that uses information from positive control spots to correct for spatial trends on the array beyond additive background. This method uses a generalized additive model to estimate a smoothed surface from positive controls. When positive controls are printed in a dilution series, a nested surface adjustment performs an intensity-based correction. When applicable, surface adjustment is able to remove spatial trends and increase within slide replicate agreement better than background subtraction alone as demonstrated on two sets of arrays. This work demonstrates the importance of including positive control spots on the array.