Variable slope normalization of reverse phase protein arrays
Variable slope normalization of reverse phase protein arrays
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DOI：
10.1093/bioinformatics/btp174
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发表时间：
2009-06-01
期刊：
影响因子：
5.8
通讯作者：
Baggerly, Keith A.
中科院分区：
文献类型：
--
作者：
Neeley, E. Shannon;Kornblau, Steven M.;Baggerly, Keith A.
动机：反相蛋白阵列（RPPA）可以同时测量一种蛋白在许多样品中的相对表达水平。一组相同斑点阵列可以用来测量一种以上蛋白质的水平。通过借用所有样品的强度来估计阵列上每个样品中的蛋白质表达，但仅使用阵列内的信息。当在不同的载玻片间进行比较时，必须考虑样品的装载量，即每个样品所打印的蛋白质总量。目前，总蛋白的估计要么使用管家蛋白，要么使用所有载玻片的样本中位数。当样品装载的可变性很大时，这些方法是次优的，因为它们没有考虑到每个载玻片的蛋白质表达是单独估计的这一事实。结果：我们提出了一种新的RPPA数据归一化方法，称为变斜率（VS）归一化，它考虑了这一数量。RPPA载玻片的阳离子分别进行。该方法能够更好地消除负载偏差，恢复蛋白质之间的真实相关结构。
Motivation: Reverse phase protein arrays (RPPA) measure the relative expression levels of a protein in many samples simultaneously. A set of identically spotted arrays can be used to measure the levels of more than one protein. Protein expression within each sample on an array is estimated by borrowing strength across all the samples, but using only within array information. When comparing across slides, it is essential to account for sample loading, the total amount of protein printed per sample. Currently, total protein is estimated using either a housekeeping protein or the sample median across all slides. When the variability in sample loading is large, these methods are suboptimal because they do not account for the fact that the protein expression for each slide is estimated separately.Results: We propose a new normalization method for RPPA data, called variable slope (VS) normalization, that takes into account that quanti. cation of RPPA slides is performed separately. This method is better able to remove loading bias and recover true correlation structures between proteins.