RANDOMIZE: A Web Server for Data Randomization.

Abstract

The microarray-based Illumina Infinium MethylationEpic BeadChip (Epic 850k) has become a useful and standard tool for epigenome wide deoxyribonucleic acid (DNA) methylation profiling. Data from this technology may suffer from batch effects due to improper handling of the samples during the plating process. Batch effects are a significant issue and can give rise to spurious and inaccurate results and reduction in power to detect real biological differences. Careful study design, such as randomizing the samples to uniformly distribute the samples across the factors responsible for batch effects, is crucial to address batch effects and other technical artifacts. Randomization helps to reduce the likelihood of bias and impact of difference among groups. This process of randomizing the samples can be a tedious, error-prone, and time-consuming task without a user-friendly and efficient tool. We present RANDOMIZE, a web-based application designed to perform randomization of relevant metadata to evenly distribute samples across the factors typically responsible for batch effects in DNA methylation microarrays, such as rows, chips and plates. We demonstrate that the tool is efficient, fast and easy to use. The tool is freely available online at https://coph-usf.shinyapps.io/RANDOMIZE/ and can be accessed using any web browser. Sample data and tutorial is also available with the tool.