A comprehensive comparison of normalization methods for loading control and variance stabilization of reverse-phase protein array data.

ABSTRACT: Loading control (LC) and variance stabilization of reverse-phase protein array (RPPA) data have been challenging mainly due to the small number of proteins in an experiment and the lack of reliable inherent control markers. In this study, we compare eight different normalization methods for LC and variance stabilization. The invariant marker set concept was first applied to the normalization of high-throughput gene expression data. A set of "invariant" markers are selected to create a virtual reference sample. Then all the samples are normalized to the virtual reference. We propose a variant of this method in the context of RPPA data normalization and compare it with seven other normalization methods previously reported in the literature. The invariant marker set method performs well with

SUBMITTER: Liu W 

PROVIDER: S-EPMC4213190 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature