Quick start guide for using the LVSmiRNA package in R

This document provides a brief guide to the LVSmiRNA package, which is a package for normalization of microRNA (miRNA) microarray data. There are four components to this package. These are: i) Reading in data. ii) Identify a subset of miRNAs with the smallest array-to-array variation, called LVS miRNAs. iii) Normalization using the selected reference set. iv) Summarization The LVS normalization method Calza et al. [2007] builds upon the fact that the data-driven housekeeping miRNAs that are the least variant across samples might be a good reference set for normalization. The total information extracted from probe-level intensity data of all samples is modeled as a function of array and probe effects using robust linear fit (rlm) Huber [1964]. The method selects miRNAs according to the arrayeffect statistic and residual standard deviation (SD) from the model. The modified LVS also incorporates a