A gene selection method for GeneChip array data with small sample sizes

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dc.contributor.authorChen, Zhongxue
dc.contributor.authorLiu, Qingzhong
dc.contributor.authorMcGee, Monnie
dc.contributor.authorKong, Megan
dc.contributor.authorHuang, Xudong
dc.contributor.authorDeng, Youpin
dc.contributor.authorScheuermann, Richard H.
dc.date.accessioned2022-01-25T16:31:34Z
dc.date.available2022-01-25T16:31:34Z
dc.date.issued2010-07
dc.descriptionThis article was originally published in BMC Genomics in 2011. doi:10.1186/1471-2164-12-S5-S7
dc.description.abstractIn microarray experiments with small sample sizes, it is a challenge to estimate p-values accurately and decide cutoff p-values for gene selection appropriately. Although permutation-based methods have proved to have greater sensitivity and specificity than the regular t-test, their p-values are highly discrete due to the limited number of permutations available in very small sample sizes. Furthermore, estimated permutation-based p-values for true nulls are highly correlated and not uniformly distributed between zero and one, making it difficult to use current false discovery rate (FDR)-controlling methods. Results: We propose a model-based information sharing method (MBIS) that, after an appropriate data transformation, utilizes information shared among genes. We use a normal distribution to model the mean differences of true nulls across two experimental conditions. The parameters of the model are then estimated using all data in hand. Based on this model, p-values, which are uniformly distributed from true nulls, are calculated. Then, since FDR-controlling methods are generally not well suited to microarray data with very small sample sizes, we select genes for a given cutoff p-value and then estimate the false discovery rate. Conclusion: Simulation studies and analysis using real microarray data show that the proposed method, MBIS, is more powerful and reliable than current methods. It has wide application to a variety of situations.
dc.description.sponsorshipNIH grant (UL1 RR024148), awarded to the University of Texas Health Science Center at Houston.
dc.description.subjectmicroarray data
dc.description.subjectmodel-based information sharing (MBIS)
dc.identifier.citationChen et al.: A gene selection method for GeneChip array data with small sample sizes. BMC Genomics 2011 12(Suppl 5):S7. doi:10.1186/1471-2164-12-S5-S7
dc.identifier.urihttps://hdl.handle.net/20.500.11875/3259
dc.language.isoen
dc.subjectmicroarray experiments
dc.subjectpermutation-based methods
dc.subjectinformation shared among genes
dc.subjectfalse discovery rate (FDR)
dc.subjectgene selection
dc.titleA gene selection method for GeneChip array data with small sample sizes
dc.typeArticle

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