Spatial normalization of reverse phase protein array data

Poorvi Kaushik, Evan J. Molinelli, Martin L. Miller, Weiqing Wang, Anil Korkut, Wenbin Liu, Zhenlin Ju, Yiling Lu, Gordon Mills, Chris Sander

Research output: Contribution to journalArticle

9 Scopus citations

Abstract

Reverse phase protein arrays (RPPA) are an efficient, high-throughput, cost-effective method for the quantification of specific proteins in complex biological samples. The quality of RPPA data may be affected by various sources of error. One of these, spatial variation, is caused by uneven exposure of different parts of an RPPA slide to the reagents used in protein detection. We present a method for the determination and correction of systematic spatial variation in RPPA slides using positive control spots printed on each slide. The method uses a simple bi-linear interpolation technique to obtain a surface representing the spatial variation occurring across the dimensions of a slide. This surface is used to calculate correction factors that can normalize the relative protein concentrations of the samples on each slide. The adoption of the method results in increased agreement between technical and biological replicates of various tumor and cell-line derived samples. Further, in data from a study of the melanoma cell-line SKMEL-133, several slides that had previously been rejected because they had a coefficient of variation (CV) greater than 15%, are rescued by reduction of CV below this threshold in each case. The method is implemented in the R statistical programing language. It is compatible with MicroVigene and SuperCurve, packages commonly used in RPPA data analysis. The method is made available, along with suggestions for implementation, at http://bitbucket.org/rppa-preprocess/rppa-preprocess/src.

Original languageEnglish (US)
Article numbere97213
JournalPloS one
Volume9
Issue number12
DOIs
StatePublished - Dec 12 2014
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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  • Cite this

    Kaushik, P., Molinelli, E. J., Miller, M. L., Wang, W., Korkut, A., Liu, W., Ju, Z., Lu, Y., Mills, G., & Sander, C. (2014). Spatial normalization of reverse phase protein array data. PloS one, 9(12), [e97213]. https://doi.org/10.1371/journal.pone.0097213