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(Referência obtida automaticamente do Web of Science, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores.)

Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments

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Autor(es):
Ribeiro, Adele H. [1] ; Pavan Soler, Julia Maria [2] ; Hirata Jr, Roberto
Número total de Autores: 3
Afiliação do(s) autor(es):
[1] Univ Sao Paulo, Dept Comp Sci, Inst Math & Stat, Sao Paulo - Brazil
[2] Univ Sao Paulo, Dept Stat, Inst Math & Stat, Sao Paulo - Brazil
Número total de Afiliações: 2
Tipo de documento: Artigo Científico
Fonte: FRONTIERS IN GENETICS; v. 10, SEP 20 2019.
Citações Web of Science: 0
Resumo

Faced with the lack of reliability and reproducibility in omics studies, more careful and robust methods are needed to overcome the existing challenges in the multi-omics analysis. In conventional omics data analysis, signal intensity values (denoted by M and values) are estimated neglecting pixel-level uncertainties, which may reflect noise and systematic artifacts. For example, intensity values from two-color microarray data are estimated by taking the mean or median of the pixel intensities within the spot and then subjected to a within-slide normalization by LOWESS. Thus, focusing on estimation and normalization of gene expression profiles, we propose a spot quantification method that takes into account pixel-level variability. Also, to preserve relevant variation that may be removed in LOWESS normalization with poorly chosen parameters, we propose a parameter selection method that is parsimonious and considers intrinsic characteristics of microarray data, such as heteroskedasticity. The usefulness of the proposed methods is illustrated by an application to real intestinal metaplasia data. Compared with the conventional approaches, the analysis is more robust and conservative, identifying fewer but more reliable differentially expressed genes. Also, the variability preservation allowed the identification of new differentially expressed genes. Using the proposed approach, we have identified differentially expressed genes involved in pathways in cancer and confirmed some molecular markers already reported in the literature. (AU)

Processo FAPESP: 06/03227-2 - Expressão gênica em tumores do estômago e do esôfago: da biologia ao diagnóstico
Beneficiário:Luiz Fernando Lima Reis
Linha de fomento: Auxílio à Pesquisa - Temático
Processo FAPESP: 11/50761-2 - Modelos e métodos de e-Science para ciências da vida e agrárias
Beneficiário:Roberto Marcondes Cesar Junior
Linha de fomento: Auxílio à Pesquisa - Temático
Processo FAPESP: 15/01587-0 - Armazenagem, modelagem e análise de sistemas dinâmicos para aplicações em e-Science
Beneficiário:João Eduardo Ferreira
Linha de fomento: Auxílio à Pesquisa - Programa eScience e Data Science - Temático