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Alternative Probeset Definitions For Combining Microarray Data Across Studies Using Different Versions Of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, Li Zhang
Alternative Probeset Definitions For Combining Microarray Data Across Studies Using Different Versions Of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, Li Zhang
Jeffrey S. Morris
Many published microarray studies have small to moderate sample sizes, and thus have low statistical power to detect significant relationships between gene expression levels and outcomes of interest. By pooling data across multiple studies, however, we can gain power, enabling us to detect new relationships. This type of pooling is complicated by the fact that gene expression measurements from different microarray platforms are not directly comparable. In this chapter, we discuss two methods for combining information across different versions of Affymetrix oligonucleotide arrays. Each involves a new approach for combining probes on the array into probesets. The first approach involves …
Some Statistical Issues In Microarray Gene Expression Data, Matthew S. Mayo, Byron J. Gajewski, Jeffrey S. Morris
Some Statistical Issues In Microarray Gene Expression Data, Matthew S. Mayo, Byron J. Gajewski, Jeffrey S. Morris
Jeffrey S. Morris
In this paper we discuss some of the statistical issues that should be considered when conducting experiments involving microarray gene expression data. We discuss statistical issues related to preprocessing the data as well as the analysis of the data. Analysis of the data is discussed in three contexts: class comparison, class prediction and class discovery. We also review the methods used in two studies that are using microarray gene expression to assess the effect of exposure to radiofrequency (RF) fields on gene expression. Our intent is to provide a guide for radiation researchers when conducting studies involving microarray gene expression …
Shrinkage Estimation For Sage Data Using A Mixture Dirichlet Prior, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes
Shrinkage Estimation For Sage Data Using A Mixture Dirichlet Prior, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes
Jeffrey S. Morris
Serial Analysis of Gene Expression (SAGE) is a technique for estimating the gene expression profile of a biological sample. Any efficient inference in SAGE must be based upon efficient estimates of these gene expression profiles, which consist of the estimated relative abundances for each mRNA species present in the sample. The data from SAGE experiments are counts for each observed mRNA species, and can be modeled using a multinomial distribution with two characteristics: skewness in the distribution of relative abundances and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample will fail …
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.