Development of a robust classifier for quality control of reverse-phase protein arrays.
BACKGROUND
High-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in approximately 1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing and amplified detection) may create substantial variability in data quality. We are not aware of any other quality control algorithm that is tuned to the special characteristics of RPPAs.


RESULTS
We have developed a novel classifier for quality control of RPPA experiments using a generalized linear model and logistic function. The outcome of the classifier, ranging from 0 to 1, is defined as the probability that a slide is of good quality. After training, we tested the classifier using two independent validation datasets. We conclude that the classifier can distinguish RPPA slides of good quality from those of poor quality sufficiently well such that normalization schemes, protein expression patterns and advanced biological analyses will not be drastically impacted by erroneous measurements or systematic variations.


METHODS
The classifier, implemented in the "SuperCurve" R package, can be freely downloaded at http://bioinformatics.mdanderson.org/main/OOMPA:Overview or http://r-forge.r-project.org/projects/supercurve/. The data used to develop and validate the classifier are available at http://bioinformatics.mdanderson.org/MOAR.
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Zhenlin
Z
Ju
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Wenbin
W
Liu
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Paul L
PL
Roebuck
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Doris R
DR
Siwak
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Nianxiang
N
Zhang
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Yiling
Y
Lu
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Michael A
MA
Davies
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Rehan
R
Akbani
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
John N
JN
Weinstein
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Gordon B
GB
Mills
Department of Bioinformatics and Computational Biology, Department of Systems Biology and Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Kevin R
KR
Coombes
D000465:Algorithms; D040081:Protein Array Analysis / Q000379:methods*; D040901:Proteomics / Q000379:methods*; D011786:Quality Control; D012984:Software