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Physical Sciences and Mathematics Commons™
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Full-Text Articles in Physical Sciences and Mathematics
Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida
Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida
Jeffrey S. Morris
We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings experimentally determined to work well in most situations. These values can be changed by the user if desired. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection, and visual data quality assessment.
An Introduction To High-Throughput Bioinformatics Data, Keith A. Baggerly, Kevin R. Coombes, Jeffrey S. Morris
An Introduction To High-Throughput Bioinformatics Data, Keith A. Baggerly, Kevin R. Coombes, Jeffrey S. Morris
Jeffrey S. Morris
High throughput biological assays supply thousands of measurements per sample, and the sheer amount of related data increases the need for better models to enhance inference. Such models, however, are more effective if they take into account the idiosyncracies associated with the specific methods of measurement: where the numbers come from. We illustrate this point by describing three different measurement platforms: microarrays, serial analysis of gene expression (SAGE), and proteomic mass spectrometry.
Bayesian Mixture Models For Gene Expression And Protein Profiles, Michele Guindani, Kim-Anh Do, Peter Mueller, Jeffrey S. Morris
Bayesian Mixture Models For Gene Expression And Protein Profiles, Michele Guindani, Kim-Anh Do, Peter Mueller, Jeffrey S. Morris
Jeffrey S. Morris
We review the use of semi-parametric mixture models for Bayesian inference in high throughput genomic data. We discuss three specific approaches for microarray data, for protein mass spectrometry experiments, and for SAGE data. For the microarray data and the protein mass spectrometry we assume group comparison experiments, i.e., experiments that seek to identify genes and proteins that are differentially expressed across two biologic conditions of interest. For the SAGE data example we consider inference for a single biologic sample.
Analysis Of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Keith A. Baggerly, Kevin R. Coombes
Analysis Of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models, Jeffrey S. Morris, Philip J. Brown, Keith A. Baggerly, Kevin R. Coombes
Jeffrey S. Morris
In this chapter, we demonstrate how to analyze MALDI-TOF/SELDITOF mass spectrometry data using the wavelet-based functional mixed model introduced by Morris and Carroll (2006), which generalizes the linear mixed models to the case of functional data. This approach models each spectrum as a function, and is very general, accommodating a broad class of experimental designs and allowing one to model nonparametric functional effects for various factors, which can be conditions of interest (e.g. cancer/normal) or experimental factors (blocking factors). Inference on these functional effects allows us to identify protein peaks related to various outcomes of interest, including dichotomous outcomes, categorical …