Brief. Bioinformatics - Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies.

Tópicos

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Resumo

It is common and advised practice in biomedical research to validate experimental or observational findings in a population different from the one where the findings were initially assessed. This practice increases the generalizability of the results and decreases the likelihood of reporting false-positive findings. Validation becomes critical when dealing with high-throughput experiments, where the large number of tests increases the chance to observe false-positive results. In this article, we review common approaches to determine statistical thresholds for validation and describe the factors influencing the proportion of significant findings from a 'training' sample that are replicated in a 'validation' sample. We refer to this proportion as rediscovery rate (RDR). In high-throughput studies, the RDR is a function of false-positive rate and power in both the training and validation samples. We illustrate the application of the RDR using simulated data and real data examples from metabolomics experiments. We further describe an online tool to calculate the RDR using t-statistics. We foresee two main applications. First, if the validation study has not yet been collected, the RDR can be used to decide the optimal combination between the proportion of findings taken to validation and the size of the validation study. Secondly, if a validation study has already been done, the RDR estimated using the training data can be compared with the observed RDR from the validation data; hence, the success of the validation study can be assessed.

Resumo Limpo

common advis practic biomed research valid experiment observ find popul differ one find initi assess practic increas generaliz result decreas likelihood report falseposit find valid becom critic deal highthroughput experi larg number test increas chanc observ falseposit result articl review common approach determin statist threshold valid describ factor influenc proport signific find train sampl replic valid sampl refer proport rediscoveri rate rdr highthroughput studi rdr function falseposit rate power train valid sampl illustr applic rdr use simul data real data exampl metabolom experi describ onlin tool calcul rdr use tstatist forese two main applic first valid studi yet collect rdr can use decid optim combin proport find taken valid size valid studi second valid studi alreadi done rdr estim use train data can compar observ rdr valid data henc success valid studi can assess

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