MmPalateMiRNA-package: R package compendium for the analysis of murine palate two-color miRNA expression data

Description

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.

Arguments

Details

Package:

MmPalateMiRNA

Type:

Package

Version:

1.0

Date:

2011-09-14

License:

LGPL

LazyLoad:

yes

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 fixOutliers and fixMVs functions, depend on the replicated structure of Miltenyi Biotech miRXplore Microarrays. Additionally, methods are available to produce diagnostic plots for RGList objects and lists of normalized data sets (MAList and / or NChannelSet objects), which build on the generic functions in lattice. 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.

References

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.