Pipeline for integrated microarray expression normalization tool kit (PIMENTo) for tumor microarray profiling experiments

Thomas Nash, Matthew Huff, W. Bailey Glen, Gary Hardiman*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

We have developed a Pipeline for Integrated Microarray Expression & Normalization Tool kit (PIMENTo) with the aim of streamlining the processes necessary for gene expression analysis in tumor tissue using DNA microarrays. Built with the R programming language and leveraging several open-source packages available through CRAN and Bioconductor, PIMENTo enables researchers to perform complex tasks with a minimal number of operations. Here, we describe the pipeline, review necessary data inputs, examine data outputs and quality control assessments and explore the commands to perform such analysis.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.,U.S.
Pages153-168
Number of pages16
DOIs
Publication statusPublished - 01 Jan 2019

Publication series

NameMethods in Molecular Biology
Volume1908
ISSN (Print)1064-3745

Keywords

  • Genomic profiling
  • Illumina Bead arrays
  • Microarrays
  • Normalization
  • Quality control
  • R
  • Tumor

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Fingerprint Dive into the research topics of 'Pipeline for integrated microarray expression normalization tool kit (PIMENTo) for tumor microarray profiling experiments'. Together they form a unique fingerprint.

  • Cite this

    Nash, T., Huff, M., Glen, W. B., & Hardiman, G. (2019). Pipeline for integrated microarray expression normalization tool kit (PIMENTo) for tumor microarray profiling experiments. In Methods in Molecular Biology (pp. 153-168). (Methods in Molecular Biology; Vol. 1908). Humana Press Inc.,U.S.. https://doi.org/10.1007/978-1-4939-9004-7_11