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IsoGeneGUI: Multiple approaches for dose-response analysis of microarray data using R

Research output: Contribution to journalArticleResearchpeer review

Authors

  • Martin Otava
  • Rudradev Sengupta
  • Ziv Shkedy
  • Dan Lin
  • Ludwig A. Hothorn

Research Organisations

External Research Organisations

  • Hasselt University
  • GlaxoSmithKline Pharmaceuticals SA/NV
  • Politeknik Statistika STIS
  • Karolinska Institutet
  • Open Analytics NV
  • PXL University of Applied Sciences and Arts
  • University of Canterbury
  • Utrecht University
  • Medical University of Vienna
  • University of Durham

Details

Original languageEnglish
Pages (from-to)14-26
Number of pages13
JournalR Journal
Volume9
Issue number1
Publication statusPublished - 10 May 2017

Abstract

The analysis of transcriptomic experiments with ordered covariates, such as dose-response data, has become a central topic in bioinformatics, in particular in omics studies. Consequently, multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various perspectives under the assumption of order restriction. We introduce the new R package IsoGene Graphical User Interface (IsoGeneGUI), an extension of the original IsoGene package that includes methods from most of available R packages designed for the analysis of order restricted microarray data, namely orQA, ORIClust, goric and ORCME. The methods included in the new IsoGeneGUI range from inference and estimation to model selection and clustering tools. The IsoGeneGUI is not only the most complete tool for the analysis of order restricted microarray experiments available in R but also it can be used to analyse other types of dose-response data. The package provides all the methods in a user friendly fashion, so analyses can be implemented by users with limited knowledge of R programming.

ASJC Scopus subject areas

Cite this

IsoGeneGUI: Multiple approaches for dose-response analysis of microarray data using R. / Otava, Martin; Sengupta, Rudradev; Shkedy, Ziv et al.
In: R Journal, Vol. 9, No. 1, 10.05.2017, p. 14-26.

Research output: Contribution to journalArticleResearchpeer review

Otava, M, Sengupta, R, Shkedy, Z, Lin, D, Pramana, S, Verbeke, T, Haldermans, P, Hothorn, LA, Gerhard, D, Kuiper, RM, Klinglmueller, F & Kasim, A 2017, 'IsoGeneGUI: Multiple approaches for dose-response analysis of microarray data using R', R Journal, vol. 9, no. 1, pp. 14-26. https://doi.org/10.32614/rj-2017-002
Otava, M., Sengupta, R., Shkedy, Z., Lin, D., Pramana, S., Verbeke, T., Haldermans, P., Hothorn, L. A., Gerhard, D., Kuiper, R. M., Klinglmueller, F., & Kasim, A. (2017). IsoGeneGUI: Multiple approaches for dose-response analysis of microarray data using R. R Journal, 9(1), 14-26. https://doi.org/10.32614/rj-2017-002
Otava M, Sengupta R, Shkedy Z, Lin D, Pramana S, Verbeke T et al. IsoGeneGUI: Multiple approaches for dose-response analysis of microarray data using R. R Journal. 2017 May 10;9(1):14-26. doi: 10.32614/rj-2017-002
Otava, Martin ; Sengupta, Rudradev ; Shkedy, Ziv et al. / IsoGeneGUI : Multiple approaches for dose-response analysis of microarray data using R. In: R Journal. 2017 ; Vol. 9, No. 1. pp. 14-26.
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