Spatial normalization of reverse phase protein array data Journal Article


Authors: Kaushik, P.; Molinelli, E. J.; Miller, M. L.; Wang, W.; Korkut, A.; Liu, W.; Ju, Z.; Lu, Y.; Mills, G.; Sander, C.
Article Title: Spatial normalization of reverse phase protein array data
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.
Keywords: reproducibility; accuracy; protein analysis; analytic method; cancer cell; melanoma cell; reliability; calculation; mathematical analysis; reverse phase protein array; article
Journal Title: PLoS ONE
Volume: 9
Issue: 12
ISSN: 1932-6203
Publisher: Public Library of Science  
Date Published: 2014-12-12
Start Page: e97213
Language: English
DOI: 10.1371/journal.pone.0097213
PROVIDER: scopus
PMCID: PMC4264691
PUBMED: 25501559
DOI/URL:
Notes: Export Date: 2 January 2015 -- Source: Scopus
Altmetric Score
MSK Authors
  1. Martin Lee Miller
    14 Miller
  2. Anil Korkut
    6 Korkut
  3. Wei-Qing Wang
    9 Wang
  4. Chris Sander
    196 Sander