A Population Proportion approach for ranking differentially expressed genes
نویسندگان
چکیده
منابع مشابه
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach.
High-dimensional case-control analysis is encountered in many different settings in genomics. In order to rank genes accordingly, many different scores have been proposed, ranging from ad hoc modifications of the ordinary t statistic to complicated hierarchical Bayesian models. Here, we introduce the "shrinkage t" statistic that is based on a novel and model-free shrinkage estimate of the varia...
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MOTIVATION The proportion of non-differentially expressed genes (pi(0)) is an important quantity in microarray data analysis. Although many statistical methods have been proposed for its estimation, it is still necessary to develop more efficient methods. METHODS Our approach for improving pi(0) estimation is to modify an existing simple method by introducing artificial censoring to P-values....
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Differentially expressed genes are usually identified by comparing steady-state mRNA concentrations. Several methods have been used for this purpose, including differential hybridization, cDNA subtraction, differential display and, more recently, DNA chips. Subtractive hybridization has significantly improved after the polymerase chain reaction was incorporated into the original method and many...
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Consider a gene expression array study comparing two groups of subjects where the goal is to explore a large number of genes in order to select for further investigation a subset that appear to be differently expressed. There has been much statistical research into the development of formal methods for designating genes as differentially expressed. These procedures control error rates such as t...
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MOTIVATION RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the gene expression omnibus do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single re...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2008
ISSN: 1471-2105
DOI: 10.1186/1471-2105-9-380