R package compendium for the analysis of two-color miRNA expression data, during the period of murine embryonic palate development (gestational days (GD) 12, 13, and 14). Samples were hybridized to Miltenyi Biotech miRXplore Microarrays. The compendium covers a wide range of steps which occur in a typical miRNA microarray data analysis, including pre-processing, normalization, differential expression analysis, clustering, target identification, and gene-set enrichment analysis.
The package contains several functions which are helpful during the
pre-processing steps of array data, which are specific to
RGList objects and, in the case of the
fixMVs functions, depend on
the replicated structure of Miltenyi Biotech miRXplore
Microarrays. Additionally, methods are available to produce diagnostic plots
RGList objects and lists of
normalized data sets (
MAList and /
NChannelSet objects), which
build on the generic functions in
Lastly, the main focus of the package is the package
vignette "MmPalateMiRNA", which contains an extended example covering
the typical steps in an miRNA microarray data analysis.
Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Bob Green, M. Michele Pisano Maintainer: Guy Brock <email@example.com>
P. Mukhopadhyay, G. Brock, V. Pihur, C. Webb, M.M. Pisano, and R.M. Greene. Developmental microRNA expression profiling of murine embryonic orofacial tissue. Birth Defects Res A Clin Mol Teratol, 88(7):511-34, 2010.
R. Gentleman. Reproducible research: a bioinformatics case study. Stat Appl Genet Mol Biol, 4:Article2, 2005.
D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. K. Godwin, C. Drescher, W. Huber, R. Gentleman, and M. Tewari. Quality assessment and data analysis for microRNA expression arrays. Nucleic Acids Res, 37(2):e17, 2009.