Introduction

High-throughput gene expression microarrays are currently the most efficient method for transcriptome-wide expression analyses. Consequently, gene expression data available through public repositories have largely been obtained from microarray experiments. However, the metadata associated with many publicly available expression microarray datasets often lacks sample sex information, therefore limiting the reuse of these data in new analyses or larger meta-analyses where the effect of sex is to be considered. Here, we present the massiR package, which provides a method for researchers to predict the sex of samples in microarray datasets. Using information from microarray probes representing Y chromosome genes, this package implements unsupervised clustering methods to classify samples into male and female groups, providing an efficient way to identify or confirm the sex of samples in mammalian microarray datasets.massiR is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org and are provided under a GPL-2 license.

Publications

  1. massiR: a method for predicting the sex of samples in gene expression microarray datasets.
    Cite this
    Buckberry S, Bent SJ, Bianco-Miotto T, Roberts CT, 2014-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Sam Buckberry
    Developer

    The Robinson Research Institute, School of Paediatrics and Reproductive Health, Australia

  2. Stephen J Bent
    Developer

    The Robinson Research Institute, School of Paediatrics and Reproductive Health, Australia

  3. Tina Bianco-Miotto
    Developer

    The Robinson Research Institute, School of Paediatrics and Reproductive Health, Australia

  4. Claire T Roberts
    Investigator

    The Robinson Research Institute, School of Paediatrics and Reproductive Health, Australia

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006606
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionAustralia
Submitted ByClaire T Roberts