Paper Info
Title
Development of a robust classifier for quality control of reverse-phase protein arrays.
Abstract
Motivation: 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.
Year
DOI
Venue
2015
10.1093/bioinformatics/btu736
BIOINFORMATICS
Field
DocType
Volume
Data mining,Control algorithm,Normalization (statistics),Data quality,Computer science,Ranging,Software,Bioinformatics,Classifier (linguistics),Protein microarray,R package
Journal
31
Issue
ISSN
Citations 
6
1367-4803
0
PageRank 
References 
Authors
0.34
0
11
Name
Order
Citations
PageRank
Zhenlin Ju110.73
Wenbin Liu200.34
Paul L Roebuck300.34
Doris R Siwak400.34
Nianxiang Zhang500.34
Yiling Lu6273.68
Michael A Davies731.04
Rehan Akbani833116.88
John N Weinstein900.34
Gordon B Mills101018.35
Kevin Coombes1129456.27