Title: SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis,
Abstract: Bakground: With the proliferation of available microarray and high throughput
sequencing experiments in the public domain, the use of meta-analysis methods
increases. In these experiments, where the sample size is often limited,
meta-analysis offers the possibility to considerably enhance the statistical
power and give more accurate results. For those purposes, it combines either
effect sizes or results of single studies in a appropriate manner. R packages
metaMA and metaRNASeq perform meta-analysis on microarray and NGS data,
respectively. They are not interchangeable as they rely on statistical modeling
specific to each technology.
Results: SMAGEXP (Statistical Meta-Analysis for Gene EXPression) integrates
metaMA and metaRNAseq packages into Galaxy. We aim to propose a unified way to
carry out meta-analysis of gene expression data, while taking care of their
specificities. We have developed this tool suite to analyse microarray data
from Gene Expression Omnibus (GEO) database or custom data from affymetrix
microarrays. These data are then combined to carry out meta-analysis using
metaMA package. SMAGEXP also offers to combine raw read counts from Next
Generation Sequencing (NGS) experiments using DESeq2 and metaRNASeq package. In
both cases, key values, independent from the technology type, are reported to
judge the quality of the meta-analysis. These tools are available on the Galaxy
main tool shed. Source code, help and installation instructions are available
on github.
Conclusion: The use of Galaxy offers an easy-to-use gene expression
meta-analysis tool suite based on the metaMA and metaRNASeq packages.