Microarray Meta Analysis
How to perform the meta-analysis of 15 GEO dataset in R. Is there any good and simple package which can be understood easily by me.
Are you a first-grade student? Graduate student? Master, PhD, post-doctoral researcher? I will assume you are at PhD / post-doctoral level:
There are several methods and papers (for example, Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline and Comparison study of microarray meta-analysis methods).
Are all the 15 GEO sets from the same microarray platform, or different platforms? Probably the most challenging part is to annotate all platforms to a common denominator.
There are indeed several R/BioConductor packages, for example, GeneMeta, crossmeta or RankProd. As you don't give details about the datasets you want to analyse, it is up to you to explore these packages and find out which one is more fit to your needs. There is also at least one server to perform meta-analyses of gene-expression (NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data).
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