MAAMD: A Workflow to Standardize Meta-Analyses of Affymetrix Microarray Data

摘要

Background: As more and more microarray data sets are available to the public, the opportunities to conduct data meta-analyses increase. Meta-analyses of microarray data consist of general steps such as downloading, decompressing, classifying, quality controlling and normalizing. These steps are time-consuming if they are not automated. A workflow is needed to automate these general steps, improve the efficiency and standardize the analyses. Methods: We constructed an extensible workflow, MAAMD, to facilitate and standardize Affymetrix meta-analyses using Kepler, an open-source software that supports user-customized scientific workflows. MAAMD incorporates two free stand-alone software tools: R and AltAnalyze, a Python based free tool for microarray and RNA-Seq analysis. The input of MAAMD is a user-supplied local CSV file, which specifies the download URL, sample information, group information (e.g. case and control) of the Affymetrix microarray data set and the target output directory. In MAAMD, the Affymetrix microarray data set is downloaded, decompressed and stored locally. The data is then classified by user-specified input information and quality-controlled using affyQCReport packages in R, followed by a selection of data by users based on the result of quality-control analysis. The selected data is then analyzed with AltAnalyze, obtaining reports of clustering, principle component analyses and statistical enrichment analysis. Results: We used MAAMD to conduct a meta-analysis of gene expression changes caused by hypoxic exposure in humans and mice. Multiple data sets such as GSE480, GSE1873 from the NCBI Gene Expression Omnibus (GEO) were successfully downloaded, quality controlled and analyzed by simply editing the CSV file. Conclusion: MAAMD workflow saves significant time and offers a standardized procedure for users to analyze multiple Affymetrix datasets. It is customizable and extensible by individual users through Kepler.