Dataset Information

Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.

ABSTRACT: DREAM is an initiative that allows researchers to assess how well their methods or approaches can describe and predict networks of interacting molecules [1]. Each year, recently acquired datasets are released to predictors ahead of publication. Researchers typically have about three months to predict the masked data or network of interactions, using any predictive method. Predictions are assessed prior to an annual conference where the best predictions are unveiled and discussed. Here we present the strategy we used to make a winning prediction for the DREAM3 phosphoproteomics challenge. We used Amelia II, a multiple imputation software method developed by Gary King, James Honaker and Matthew Blackwell[2] in the context of social sciences to predict the 476 out of 4624 measurements that had been masked for the challenge. To chose the best possible multiple imputation parameters to apply for the challenge, we evaluated how transforming the data and varying the imputation parameters affected the ability to predict additionally masked data. We discuss the accuracy of our findings and show that multiple imputations applied to this dataset is a powerful method to accurately estimate the missing data. We postulate that multiple imputations methods might become an integral part of experimental design as a mean to achieve cost savings in experimental design or to increase the quantity of samples that could be handled for a given cost.

SUBMITTER: Guex N

PROVIDER: S-EPMC2807461 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature

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Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.

Guex Nicolas N Migliavacca Eugenia E Xenarios Ioannis I

PloS one 20100118 1

DREAM is an initiative that allows researchers to assess how well their methods or approaches can describe and predict networks of interacting molecules [1]. Each year, recently acquired datasets are released to predictors ahead of publication. Researchers typically have about three months to predict the masked data or network of interactions, using any predictive method. Predictions are assessed prior to an annual conference where the best predictions are unveiled and discussed. Here we present ...[more]

PMID: 20090915

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Project description:Accurately estimating the period of time that individuals are exposed to online intervention content is important for understanding program engagement. This can be calculated from time-stamped data reflecting navigation to and from individual webpages. Prolonged periods of inactivity are commonly handled with a time-out feature and assigned a prespecified exposure duration. Unfortunately, this practice can lead to biased results describing program exposure.The aim of the study was to describe how multiple imputations can be used to better account for the time spent viewing webpages that result in a prolonged period of inactivity or a time-out.To illustrate this method, we present data on time-outs collected from the Q(2) randomized smoking cessation trial. For this analysis, we evaluate the effects on intervention exposure of receiving content written in a prescriptive versus motivational tone. Using multiple imputations, we created five complete datasets in which the time spent viewing webpages that resulted in a time-out were replaced with values estimated with imputation models. We calculated standard errors using Rubin's formulas to account for the variability due to the imputations. We also illustrate how current methods of accounting for time-outs (excluding timed-out page views or assigning an arbitrary viewing time) can influence conclusions about participant engagement.A total of 63.00% (1175/1865) of participants accessed the online intervention in the Q(2) trial. Of the 6592 unique page views, 683 (10.36%, 683/6592) resulted in a time-out. The median time spent viewing webpages that did not result in a time-out was 1.07 minutes. Assuming participants did not spend any time viewing a webpage that resulted in a time-out, no difference between the two message tones was observed (ratio of mean time online: 0.87, 95% CI 0.75-1.02). Assigning 30 minutes of viewing time to all page views that resulted in a time-out concludes that participants who received content in a motivational tone spent less time viewing content (ratio of mean time online: 0.86, 95% CI 0.77-0.98) than those participants who received content in a prescriptive tone. Using multiple imputations to account for time-outs concludes that there is no difference in participant engagement between the two message tones (ratio of mean time online: 0.87; 95% CI 0.75-1.01).The analytic technique chosen can significantly affect conclusions about online intervention engagement. We propose a standardized methodology in which time spent viewing webpages that result in a time-out is treated as missing information and corrected with multiple imputations.Clinicaltrials.gov NCT00992264; http://clinicaltrials.gov/ct2/show/NCT00992264 (Archived by WebCite at http://www.webcitation.org/6Kw5m8EkP).

Dataset Information

Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.

Publications

Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy.

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