Oligomask

A framework for assessing and removing the effect of genetic variants on microarray probes

Daniel Bottomly, Beth Wilmot, Shannon McWeeney

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

As expression microarrays are typically designed relative to a reference genome, any individual genetic variant that overlaps a probe's genomic position can possibly cause a reduction in hybridization due to the probe no longer being a perfect match to a given sample's mRNA at that locus. If the samples or groups used in a microarray study differ in terms of genetic variants, the results of the microarray experiment can be negatively impacted. The oligoMask package is an R/SQLite framework which can utilize publicly available genetic variants and works in conjunction with the oligo package to read in the expression data and remove microarray probes which are likely to impact a given microarray experiment prior to analysis. Tools are provided for creating an SQLite database containing the probe and variant annotations and for performing the commonly used RMA preprocessing procedure for Affymetrix microarrays.

Original languageEnglish (US)
Pages (from-to)159-163
Number of pages5
JournalR Journal
Volume6
Issue number1
StatePublished - 2014

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Microarrays
Microarray
Probe
Messenger RNA
Experiment
Genomics
Preprocessing
Annotation
Locus
Framework
Overlap
Genome
Genes
Experiments
Likely

ASJC Scopus subject areas

  • Statistics and Probability
  • Numerical Analysis
  • Statistics, Probability and Uncertainty

Cite this

Oligomask : A framework for assessing and removing the effect of genetic variants on microarray probes. / Bottomly, Daniel; Wilmot, Beth; McWeeney, Shannon.

In: R Journal, Vol. 6, No. 1, 2014, p. 159-163.

Research output: Contribution to journalArticle

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