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Introduction of a new critical p value correction method for statistical significance analysis of metabonomics data.

ABSTRACT: Nuclear magnetic resonance (NMR) spectroscopy-based metabonomics is of growing importance for discovery of human disease biomarkers. Identification and validation of disease biomarkers using statistical significance analysis (SSA) is critical for translation to clinical practice. SSA is performed by assessing a null hypothesis test using a derivative of the Student's t test, e.g., a Welch's t test. Choosing how to correct the significance level for rejecting null hypotheses in the case of multiple testing to maintain a constant family-wise type I error rate is a common problem in such tests. The multiple testing problem arises because the likelihood of falsely rejecting the null hypothesis, i.e., a false positive, grows as the number of tests applied to the same data set increases. Several methods have been introduced to address this problem. Bonferroni correction (BC) assumes all variables are independent and therefore sacrifices sensitivity for detecting true positives in partially dependent data sets. False discovery rate (FDR) methods are more sensitive than BC but uniformly ascribe highest stringency to lowest p value variables. Here, we introduce standard deviation step down (SDSD), which is more sensitive and appropriate than BC for partially dependent data sets. Sensitivity and type I error rate of SDSD can be adjusted based on the degree of variable dependency. SDSD generates fundamentally different profiles of critical p values compared with FDR methods potentially leading to reduced type II error rates. SDSD is increasingly sensitive for more concentrated metabolites. SDSD is demonstrated using NMR-based metabonomics data collected on three different breast cancer cell line extracts.

SUBMITTER: Wang B

PROVIDER: S-EPMC4528961 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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Introduction of a new critical p value correction method for statistical significance analysis of metabonomics data.

Wang Bo B Shi Zhanquan Z Weber Georg F GF Kennedy Michael A MA

Analytical and bioanalytical chemistry 20130913 26

Nuclear magnetic resonance (NMR) spectroscopy-based metabonomics is of growing importance for discovery of human disease biomarkers. Identification and validation of disease biomarkers using statistical significance analysis (SSA) is critical for translation to clinical practice. SSA is performed by assessing a null hypothesis test using a derivative of the Student's t test, e.g., a Welch's t test. Choosing how to correct the significance level for rejecting null hypotheses in the case of multip ...[more]

PMID: 24026514

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Project description:The growth of COVID-19 pandemic throughout more than 213 countries around the world have put a lot of pressures on governments and health services to try to stop the rapid expansion of the pandemic. During 2009, H1N1 Influenza pandemic, statistical and mathematical methods were used to track how the virus spreads around countries. Most of these models that were developed at the beginning of the XXI century are based on the classical susceptible-infected-recovered (SIR) model developed almost a hundred years ago. The evolution of this model allows us to forecast and compute basic and effective reproduction numbers (R t and R 0 ), measures that quantify the epidemic potential of a pathogen and estimates different scenarios. In this study, we present a traditional estimation technique for R0 with statistical distributions by best fitting and a Bayesian approach based on continuous feed of prior distributions to obtain posterior distributions and computing real time Rt . We use data from COVID-19 officially reported cases in Ecuador since the first confirmed case on February 29th. Because of the lack of data, in the case of R0 we compare two methods for the estimation of these parameters below exponential growth and maximum likelihood estimation. We do not make any assumption about the evolution of cases due to limited information and we use previous methods to compare scenarios about R0 and in the case of Rt we used Bayesian inference to model uncertainty in contagious proposing a new modification to the well-known model of Bettencourt and Ribeiro based on a time window of m days to improve estimations. Ecuadorian R0 with exponential growth criteria was 3.45 and with the maximum likelihood estimation method was 2.93. The results show that Guayas, Pichincha and Manabí were the provinces with the highest number of cases due to COVID-19. Some reasons explain the increased transmissibility in these localities: massive events, population density, cities dispersion patterns, and the delayed time of public health actions to contain pandemic. In conclusion, this is a novel approach that allow us to measure infection dynamics and outbreak distribution when not enough detailed data is available. The use of this model can be used to predict pandemic distribution and to implement data-based effective measures.

Dataset Information

Introduction of a new critical p value correction method for statistical significance analysis of metabonomics data.

Publications

Introduction of a new critical p value correction method for statistical significance analysis of metabonomics data.

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