Section: Software

MetaMa

Participant : Guillemette Marot.

metaMA is a specialised software for microarrays. It is a R package which combines either p-values or modified effect sizes from different studies to find differentially expressed genes. The main competitor of metaMA is geneMeta. Compared to geneMeta, metaMA offers an improvement for small sample size datasets since the corresponding modelling is based on shrinkage approaches.

Guillemette Marot is the main contributor and the maintainer of this packages and spent around one year full time for this package between the conception, the implementation, and the documentation. Her PhD advisors (Florence Jaffrézic, Claus-Dieter Mayer, Jean-Louis Foulley) helped her with the conception but she implemented alone the code.

First versions have been posted to the CRAN, the official website of the R software, in 2009. New versions for this package were released in August 2011 in order to take into account remarks from the main users (biologists or biostatisticians analysing gene expression data). This software is routinely used by biologists from INRA, Jouy en Josas (it has been included in a local analysis pipeline) but its diffusion on the CRAN makes it available to a wider community, as attested by the publications citing the software(G. Marot,J.-L. Foulley, C.-D. Mayer, F. Jaffrézic, Moderated effect size and p-value combinations for microarray meta-analyses, in "Bioinformatics", 2009, vol. 25, no 20, p. 2692–-2699.).

More information is available on the website http://cran.r-project.org/web/packages/metaMA/