Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments

Thomas Nash; Matthew Huff; W Bailey Glen Jr; Gary Hardiman

doi:10.1007/978-1-4939-9004-7_11

Pipeline for Integrated Microarray Expression Normalization Tool Kit (PIMENTo) for Tumor Microarray Profiling Experiments

Methods Mol Biol. 2019:1908:153-168. doi: 10.1007/978-1-4939-9004-7_11.

Authors

Thomas Nash^{1

2}, Matthew Huff³, W Bailey Glen Jr^{1

4}, Gary Hardiman^{5

6

7

8}

Affiliations

¹ MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.
² Department of Computer Science, College of Charleston, Charleston, SC, USA.
³ MS in Biomedical Sciences Program, Medical University of South Carolina (MUSC), Charleston, SC, USA.
⁴ Department of Pathology and Laboratory Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA.
⁵ MUSC Bioinformatics, Center for Genomics Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. [email protected].
⁶ Department of Medicine, Medical University of South Carolina (MUSC), Charleston, SC, USA. [email protected].
⁷ Department of Public Health Sciences, Medical University of South Carolina (MUSC), Charleston, SC, USA. [email protected].
⁸ School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Stranmillis Road, Belfast, BT9 5AG, UK. [email protected].

PMID: 30649727
DOI: 10.1007/978-1-4939-9004-7_11

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.

Keywords: Genomic profiling; Illumina Bead arrays; Microarrays; Normalization; Quality control; R; Tumor.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Gene Expression Profiling / methods*
Gene Expression Regulation, Neoplastic
Humans
Neoplasms / genetics*
Oligonucleotide Array Sequence Analysis / methods*
Quality Control
RNA, Neoplasm
Sequence Analysis, RNA / methods
Software*

Substances

RNA, Neoplasm