MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm

BMC Bioinformatics

Software

Wei-Sheng Wu¹  Meng-Jhun Jhou¹ 

[1] Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan;

关键词: Web tool;    Missing value imputation;    Microarray data;    Performance index;    Performance comparison;    Algorithm;   

DOI  :  10.1186/s12859-016-1429-3

 received in 2016-05-15, accepted in 2016-12-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMissing value imputation is important for microarray data analyses because microarray data with missing values would significantly degrade the performance of the downstream analyses. Although many microarray missing value imputation algorithms have been developed, an objective and comprehensive performance comparison framework is still lacking. To solve this problem, we previously proposed a framework which can perform a comprehensive performance comparison of different existing algorithms. Also the performance of a new algorithm can be evaluated by our performance comparison framework. However, constructing our framework is not an easy task for the interested researchers. To save researchers’ time and efforts, here we present an easy-to-use web tool named MVIAeval (Missing Value Imputation Algorithm evaluator) which implements our performance comparison framework.ResultsMVIAeval provides a user-friendly interface allowing users to upload the R code of their new algorithm and select (i) the test datasets among 20 benchmark microarray (time series and non-time series) datasets, (ii) the compared algorithms among 12 existing algorithms, (iii) the performance indices from three existing ones, (iv) the comprehensive performance scores from two possible choices, and (v) the number of simulation runs. The comprehensive performance comparison results are then generated and shown as both figures and tables.ConclusionsMVIAeval is a useful tool for researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be represented as a matrix form (e.g. NGS data or proteomics data). Thus, MVIAeval will greatly expedite the progress in the research of missing value imputation algorithms.

【 授权许可】

CC BY   
© The Author(s). 2017