Skip to main content

A Comparison of Arraystar and the Open-Source Software R for the Statistical Analysis of Microarray Data

Presented by:
Julia Jamison
Abstract:

The fruit fly Drosophila melanogaster is among one of the most extensively studied organisms in genomic history serving as a robust model in studying human biology. Microarray technology and development has proven to be an efficient and cost effective method of gene expression analysis. An analysis of microarray data showing the most differentially expressed genes in the fruit fly following tissue injury was performed using both R and DNAStar’s Arraystar software package in order to identify differences between a freely available, open-source software, and a licensed gene expression analysis software.  We compared the RNA of non-injured flies (control) to the RNA of flies that were injured prior to their pubic state (ablated).  In the analysis, we aimed to detail which, if any, genes had been differentially expressed. Two samples of D. melanogaster microarray data, each containing 14,973 genes, were analyzed in Arraystar and using Bioconductor’s Limma package in R. This comparison of open-sourced statistical software and specifically developed, licensed software for the analysis of these microarray data aims to increase the feasibility of rapid and efficient identification of differentially expressed genes in many fields of study, as open-source software suites such as Bioconductor are readily available to those with limited budgets and resources.  Moving forward, the developed process can be applied to study the gene expression response to other types of tissue damage using either software.