NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data

• DOI: 10.1093/bioinformatics/bts188
• Publication Date: 2012-04-19T00:25:22Z
• Authors: Daryl Waggott; Kenneth Chu; Shaoming Yin; Bradly G. Wouters; Fei-Fei Liu; Paul C. Boutros
• Keywords: R package; Sample (material); Extensibility; Data extraction

Abstract Motivation: The NanoString nCounter Platform is a new and promising technology for measuring nucleic acid abundances. It has several advantages over PCR-based techniques, including avoidance of amplification, direct sequence interrogation digital detection absolute quantification. These features minimize aspects experimental error hold promise dealing with challenging conditions such as archival formalin-fixed paraffin-embedded samples. However, systematic inter-sample technical artifacts caused by variability in sample preservation, bio-molecular extraction platform fluctuations must be removed to ensure robust data. Results: To facilitate this process address these issues datasets, we have written pre-processing package called NanoStringNorm the R statistical language. Key include an extensible environment method comparison algorithm development, integrated gene diagnostics, facilitated downstream analysis. open-source, available through CRAN repository, includes unit-tests numerical accuracy, provides visual numeric diagnostics. Availability: http://cran.r-project.org/web/packages/NanoStringNorm Contact: [e-mail] Supplementary information: data are at Bioinformatics online.