Eralp Dogu

Bio: Eralp Dogu is an academic researcher from Muğla University. The author has contributed to research in topics: Control chart & Statistical process control. The author has an hindex of 8, co-authored 13 publications receiving 106 citations. Previous affiliations of Eralp Dogu include Dokuz Eylül University & Northeastern University.

Performance of maximum EWMA control chart in the presence of measurement error using auxiliary information

Abstract: EWMA and Max-EWMA charts are considered efficient for individual as well as joint monitoring of mean and variance shifts in the production process. However, measurement error is affecting the effic...

Estimation of Change Point in Generalized Variance Control Chart

Abstract: In this study, using maximum likelihood estimation, a considerably effective change point model is proposed for the generalized variance control chart in which the required statistics are calculated with its distributional properties. The procedure, when used with generalized variance control charts, would be helpful for practitioners both controlling the multivariate process dispersion and detecting the time of the change in variance-covariance matrix of a process. The procedure starts after the chart issues a signal. Several structural changes for the variance-covariance matrix are considered and the precision and the accuracy of the proposed method is discussed.

A Multivariate Change Point Detection Procedure for Monitoring Mean and Covariance Simultaneously

Abstract: The signal issued by a control chart triggers the process professionals to investigate the special cause. Change point methods simplify the efforts to search for and identify the special cause. In this study, using maximum likelihood estimation, a multivariate joint change point estimation procedure for monitoring both location and dispersion simultaneously is proposed. After a signal is generated by the simultaneously used Hotelling's T 2 and/or generalized variance control charts, the procedure starts detecting the time of the change. The performance of the proposed method for several structural changes for the mean vector and covariance matrix is discussed.

MSstatsQC 2.0: R/Bioconductor Package for Statistical Quality Control of Mass Spectrometry-Based Proteomics Experiments.

Abstract: MSstatsQC is an R/Bioconductor package for statistical monitoring of longitudinal system suitability and quality control in mass spectrometry-based proteomics. MSstatsQC was initially designed for targeted selected reaction monitoring experiments. This paper presents an extension, MSstatsQC 2.0, that supports experiments with global data-dependent and data-independent acquisition. The extension implements data processing and analyses that are specific to these acquisition types. It relies on state-of-the-art methods of statistical process control to detect deviations from optimal performance of various metrics (such as intensity and retention time of chromatographic peaks) and to summarize the results across multiple metrics and analytes. Additionally, the web-based graphical user interface MSstatsQCgui, implemented as a separate R/Bioconductor package, provides a user-friendly way to visualize and report the results from MSstatsQC 2.0.

Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

Abstract: There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories

Abstract: The increasing number of biomedical and translational applications in mass spectrometry-based proteomics poses new analytical challenges and raises the need for automated quality control systems. Despite previous efforts to set standard file formats, data processing workflows and key evaluation parameters for quality control, automated quality control systems are not yet widespread among proteomics laboratories, which limits the acquisition of high-quality results, inter-laboratory comparisons and the assessment of variability of instrumental platforms. Here we present QCloud, a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation. QCloud supports the most common targeted and untargeted proteomics workflows, it accepts data formats from different vendors and it enables the annotation of acquired data and reporting incidences. A complete version of the QCloud system has successfully been developed and it is now open to the proteomics community (http://qcloud.crg.eu). QCloud system is an open source project, publicly available under a Creative Commons License Attribution-ShareAlike 4.0.

An Overview of Control Charts for High‐quality Processes

Abstract: Major difficulties in the study of high-quality processes with traditional process monitoring techniques are a high false alarm rate and a negative lower control limit. The purpose of time-between-events control charts is to overcome existing problems in the high-quality process monitoring setup. Time-between-events charts detect an out-of-control situation without great loss of sensitivity as compared with existing charts. High-quality control charts gained much attention over the last decade because of the technological revolution. This article is dedicated to providing an overview of recent research and presenting it in a unifying framework. To summarize results and draw a precise conclusion from the statistical point of view, cross-tabulations are also given in this article. Copyright © 2016 John Wiley & Sons, Ltd.

A multivariate control chart for simultaneously monitoring process mean and variability

Abstract: Recently, monitoring the process mean and variability simultaneously for multivariate processes by using a single control chart has drawn some attention. However, due to the complexity of multivariate distributions, existing methods in univariate processes cannot be readily extended to multivariate processes. In this paper, we propose a new single control chart which integrates the exponentially weighted moving average (EWMA) procedure with the generalized likelihood ratio (GLR) test for jointly monitoring both the multivariate process mean and variability. Due to the powerful properties of the GLR test and the EWMA procedure, the new chart provides quite robust and satisfactory performance in various cases, including detection of the decrease in variability and individual observation at the sampling point, which are very important cases in many practical applications but may not be well handled by existing approaches in the literature. The application of our proposed method is illustrated by a real data example in ambulatory monitoring.

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data

Abstract: We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides infrastructure for the manipulation, processing, and visualization of mass spectrometry data. We focus on the new on-disk infrastructure, that allows the handling of large raw mass spectrometry experiments on commodity hardware and illustrate how the package is used for elegant data processing, method development, and visualization.