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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments

Full text
Author(s):
Ribeiro, Adele H. [1] ; Pavan Soler, Julia Maria [2] ; Hirata Jr, Roberto
Total Authors: 3
Affiliation:
[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
Total Affiliations: 2
Document type: Journal article
Source: FRONTIERS IN GENETICS; v. 10, SEP 20 2019.
Web of Science Citations: 0
Abstract

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)

FAPESP's process: 06/03227-2 - Gene expression profile of tumors from the upper digestive track: from tumor biology to new diagnostic tools
Grantee:Luiz Fernando Lima Reis
Support type: Research Projects - Thematic Grants
FAPESP's process: 11/50761-2 - Models and methods of e-Science for life and agricultural sciences
Grantee:Roberto Marcondes Cesar Junior
Support type: Research Projects - Thematic Grants
FAPESP's process: 15/01587-0 - Storage, modeling and analysis of dynamical systems for e-Science applications
Grantee:João Eduardo Ferreira
Support type: Research Grants - eScience and Data Science Program - Thematic Grants