Bioconductor Infrastructure Packages for NanoString Assay Data
David Allen Henderson,Nicole Ortogero,Zhi Yang,Jason Reeves,Rona Vitancol,Patrick Aboyoun,David Allen Henderson,Kara Gorman,Thomas Smith NanoString Technologies
Abstract
Bioconductor packages to store and manage NanoString Assay data have been unavailable prior to now, leading many researchers analyzing their data outside of NanoString’s nSolver Advanced Analysis software for nCounter data with little support and no support for GeoMx data outside of NanoStrings DSP-Data Analysis Suite software. To address this need, two Bioconductor packages have been developed: NanoStringNCTools and GeomxTools. These packages are built based on the ExpressionSet R object and provide support for data loading, filtering, normalization, and use in other Bioconductor packages that are aware of ExpressionSet objects. These packages also contain plotting functions to aid in assessing normalization success and in quality control checking of assay data. General use and functionality will be demonstrated. NanoString products are for research use only.
Keywords: NanoString,nCounter,GeoMx,Spatial,gene expression