MmPalateMiRNA-package {MmPalateMiRNA} | R Documentation

## 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.

### 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.

### Author(s)

Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Bob Green, M. Michele Pisano Maintainer: Guy Brock <guy.brock@louisville.edu>

### 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.

[Package MmPalateMiRNA version 1.30.0 Index]