Dataset Information

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

ABSTRACT:

Background

With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences ("batch effects") as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies.

Focus

The current study focuses on the construction of classifiers, and the use of cross-validation to estimate their performance. In particular, we investigate the impact of batch effects and differences in sample composition between batches on the accuracy of the classification performance estimate obtained via cross-validation. The focus on estimation bias is a main difference compared to previous studies, which have mostly focused on the predictive performance and how it relates to the presence of batch effects.

Data

We work on simulated data sets. To have realistic intensity distributions, we use real gene expression data as the basis for our simulation. Random samples from this expression matrix are selected and assigned to group 1 (e.g., 'control') or group 2 (e.g., 'treated'). We introduce batch effects and select some features to be differentially expressed between the two groups. We consider several scenarios for our study, most importantly different levels of confounding between groups and batch effects.

Methods

We focus on well-known classifiers: logistic regression, Support Vector Machines (SVM), k-nearest neighbors (kNN) and Random Forests (RF). Feature selection is performed with the Wilcoxon test or the lasso. Parameter tuning and feature selection, as well as the estimation of the prediction performance of each classifier, is performed within a nested cross-validation scheme. The estimated classification performance is then compared to what is obtained when applying the classifier to independent data.

SUBMITTER: Soneson C

PROVIDER: S-EPMC4072626 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

Soneson Charlotte C Gerster Sarah S Delorenzi Mauro M

PloS one 20140626 6

<h4>Background</h4>With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences ("batch effects") as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies.<h4>Focus</h4>The current study focuses on the construction of classifier ...[more]

PMID: 24967636

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Project description:Background Confounding is a common issue in epidemiological research. Commonly used confounder-adjustment methods include multivariable regression analysis and propensity score methods. Although it is common practice to assess the linearity assumption for the exposure-outcome effect, most researchers do not assess linearity of the relationship between the confounder and the exposure and between the confounder and the outcome before adjusting for the confounder in the analysis. Failing to take the true non-linear functional form of the confounder-exposure and confounder-outcome associations into account may result in an under- or overestimation of the true exposure effect. Therefore, this paper aims to demonstrate the importance of assessing the linearity assumption for confounder-exposure and confounder-outcome associations and the importance of correctly specifying these associations when the linearity assumption is violated. Methods A Monte Carlo simulation study was used to assess and compare the performance of confounder-adjustment methods when the functional form of the confounder-exposure and confounder-outcome associations were misspecified (i.e., linearity was wrongly assumed) and correctly specified (i.e., linearity was rightly assumed) under multiple sample sizes. An empirical data example was used to illustrate that the misspecification of confounder-exposure and confounder-outcome associations leads to bias. Results The simulation study illustrated that the exposure effect estimate will be biased when for propensity score (PS) methods the confounder-exposure association is misspecified. For methods in which the outcome is regressed on the confounder or the PS, the exposure effect estimate will be biased if the confounder-outcome association is misspecified. In the empirical data example, correct specification of the confounder-exposure and confounder-outcome associations resulted in smaller exposure effect estimates. Conclusion When attempting to remove bias by adjusting for confounding, misspecification of the confounder-exposure and confounder-outcome associations might actually introduce bias. It is therefore important that researchers not only assess the linearity of the exposure-outcome effect, but also of the confounder-exposure or confounder-outcome associations depending on the confounder-adjustment method used. Supplementary Information The online version contains supplementary material available at 10.1186/s12874-022-01817-0.

Project description:BackgroundSelection bias and unmeasured confounding are fundamental problems in epidemiology that threaten study internal and external validity. These phenomena are particularly dangerous in internet-based public health surveillance, where traditional mitigation and adjustment methods are inapplicable, unavailable, or out of date. Recent theoretical advances in causal modeling can mitigate these threats, but these innovations have not been widely deployed in the epidemiological community.ObjectiveThe purpose of our paper is to demonstrate the practical utility of causal modeling to both detect unmeasured confounding and selection bias and guide model selection to minimize bias. We implemented this approach in an applied epidemiological study of the COVID-19 cumulative infection rate in the New York City (NYC) spring 2020 epidemic.MethodsWe collected primary data from Qualtrics surveys of Amazon Mechanical Turk (MTurk) crowd workers residing in New Jersey and New York State across 2 sampling periods: April 11-14 and May 8-11, 2020. The surveys queried the subjects on household health status and demographic characteristics. We constructed a set of possible causal models of household infection and survey selection mechanisms and ranked them by compatibility with the collected survey data. The most compatible causal model was then used to estimate the cumulative infection rate in each survey period.ResultsThere were 527 and 513 responses collected for the 2 periods, respectively. Response demographics were highly skewed toward a younger age in both survey periods. Despite the extremely strong relationship between age and COVID-19 symptoms, we recovered minimally biased estimates of the cumulative infection rate using only primary data and the most compatible causal model, with a relative bias of +3.8% and -1.9% from the reported cumulative infection rate for the first and second survey periods, respectively.ConclusionsWe successfully recovered accurate estimates of the cumulative infection rate from an internet-based crowdsourced sample despite considerable selection bias and unmeasured confounding in the primary data. This implementation demonstrates how simple applications of structural causal modeling can be effectively used to determine falsifiable model conditions, detect selection bias and confounding factors, and minimize estimate bias through model selection in a novel epidemiological context. As the disease and social dynamics of COVID-19 continue to evolve, public health surveillance protocols must continue to adapt; the emergence of Omicron variants and shift to at-home testing as recent challenges. Rigorous and transparent methods to develop, deploy, and diagnosis adapted surveillance protocols will be critical to their success.

Dataset Information

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

Background

Focus

Data

Methods

Publications

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

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