BackgroundUntargeted metabolomics generates a huge amount of data. Software packages for automated data processing are crucial to successfully process these data. A variety of such software packages exist, but the outcome of data processing strongly depends on algorithm parameter settings. If they are not carefully chosen, suboptimal parameter settings can easily lead to biased results. Therefore, parameter settings also require optimization. Several parameter optimization approaches have already been proposed, but a software package for parameter optimization which is free of intricate experimental labeling steps, fast and widely applicable is still missing.ResultsWe implemented the software package IPO (‘Isotopologue Parameter Optimization’) which is fast and free of labeling steps, and applicable to data from different kinds of samples and data from different methods of liquid chromatography - high resolution mass spectrometry and data from different instruments.IPO optimizes XCMS peak picking parameters by using natural, stable 13C isotopic peaks to calculate a peak picking score. Retention time correction is optimized by minimizing relative retention time differences within peak groups. Grouping parameters are optimized by maximizing the number of peak groups that show one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiments, and the resulting scores are evaluated using response surface models. IPO was tested on three different data sets, each consisting of a training set and test set. IPO resulted in an increase of reliable groups (146% - 361%), a decrease of non-reliable groups (3% - 8%) and a decrease of the retention time deviation to one third.ConclusionsIPO was successfully applied to data derived from liquid chromatography coupled to high resolution mass spectrometry from three studies with different sample types and different chromatographic methods and devices. We were also able to show the potential of IPO to increase the reliability of metabolomics data.The source code is implemented in R, tested on Linux and Windows and it is freely available for download at https://github.com/glibiseller/IPO. The training sets and test sets can be downloaded from https://health.joanneum.at/IPO.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0562-8) contains supplementary material, which is available to authorized users.

We consider Bayesian inference for regression models of count data subject to underreporting. For the data generating process of counts as well as the fallible reporting process a joint model is specified, where the outcomes in both processes are related to a set of potential covariates. Identification of the joint model is achieved by additional information provided through validation data and incorporation of variable selection. For posterior inference we propose a convenient Markov chain Monte Carlo (MCMC) sampling scheme which relies on data augmentation and auxiliary mixture sampling techniques for this two-part model. Performance of the method is illustrated for simulated data and applied to analyse real data, collected to estimate risk of cervical cancer death.

Remaining useful life (RUL) prediction is central to prognostics and reliability assessment of light-emitting diode (LED) systems. Their unknown long-term service life remaining when subject to specific operating conditions is affected by various sources of uncertainty stemming from production of individual system components, application of the whole system, measurement and operation. To enhance the reliability of model-based predictions, it is essential to account for all of these uncertainties in a systematic manner. This paper proposes a Bayesian hierarchical modelling framework for inverse uncertainty quantification (UQ) in LED operation under thermal loading. The main focus is on the LED systems’ operational thermal resistances, which are subject to system and application variability. Posterior inference is based on a Markov chain Monte Carlo (MCMC) sampling scheme using the Metropolis–Hastings (MH) algorithm. Performance of the method is investigated for simulated data, which allow to focus on different UQ aspects in applications. Findings from an application scenario in which the impact of disregarded uncertainty on RUL prediction is discussed highlight the need for a comprehensive UQ to allow for reliable predictions.

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