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Results: In this paper, we present an analysis of a typical two-color miRNA microarray experiment using publicly available packages from R and Bioconductor, the open-source software project for the analysis ... The paper is presented as a "compendium" which, along with the accompanying R package MmPalateMiRNA, contains all of the experimental data and source code to reproduce the analyses contained in the paper ... Acknowledgements This research was supported in part by NIH grants DE018215, HD053509, and P20 RR017702 from the COBRE program of the National Center for Research Resources, and DOE grant 10EM00542. ...doi:10.1186/1751-0473-8-1 pmid:23298515 pmcid:PMC3654997 fatcat:yhems64hkvbsvfzhaxsjkvnwau