RECISION.array: An R package for benchmarking microRNA array data normalization in the context of sample classification Journal Article
| Authors: | Huang, H. C.; Wu, Y.; Yang, Q.; Qin, L. X. |
| Article Title: | RECISION.array: An R package for benchmarking microRNA array data normalization in the context of sample classification |
| Abstract: | We present a new R package PRECISION.array for assessing the performance of data normalization methods in connection with methods for sample classification. It includes two microRNA microarray datasets for the same set of tumor samples: a re-sampling-based algorithm for simulating additional paired datasets under various designs of sample-to-array assignment and levels of signal-to-noise ratios and a collection of numerical and graphical tools for method performance assessment. The package allows users to specify their own methods for normalization and classification, in addition to implementing three methods for training data normalization, seven methods for test data normalization, seven methods for classifier training, and two methods for classifier validation. It enables an objective and systemic evaluation of the operating characteristics of normalization and classification methods in microRNA microarrays. To our knowledge, this is the first such tool available. The R package can be downloaded freely at https://github.com/LXQin/PRECISION.array. Copyright © 2022 Huang, Wu, Yang and Qin. |
| Keywords: | microrna; classification; benchmarking; microarray; normalization |
| Journal Title: | Frontiers in Genetics |
| Volume: | 13 |
| ISSN: | 1664-8021 |
| Publisher: | Frontiers Media S.A. |
| Date Published: | 2022-07-01 |
| Start Page: | 838679 |
| Language: | English |
| DOI: | 10.3389/fgene.2022.838679 |
| PROVIDER: | scopus |
| PMCID: | PMC9354575 |
| PUBMED: | 35938023 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 September 2022 -- Source: Scopus |
Altmetric
Citation Impact
BMJ Impact Analytics
Related MSK Work