NACHO: NAnostring quality Control dasHbOard

Abstract

The NanoStringTM nCounter® is a platform for the targeted quantification of expression data in biofluids and tissues. While software by the manufacturer is available in addition to third parties packages, they do not provide a complete quality control (QC) pipeline. Here, we present NACHO (‘NAnostring quality Control dasHbOard’), a comprehensive QC R-package. The package consists of three subsequent steps: summarize, visualize and normalize. The summarize function collects all the relevant data and stores it in a tidy format, the visualize function initiates a dashboard with plots of the relevant QC outcomes. It contains QC metrics that are measured by default by the manufacturer, but also calculates other insightful measures, including the scaling factors that are needed in the normalization step. In this normalization step, different normalization methods can be chosen to optimally preprocess data. Together, NACHO is a comprehensive method that optimizes insight and preprocessing of nCounter® data.

Date
Friday, the 6 of September, 2019
Event
Research Seminar
Location
Lausanne, Switzerland
Mickaël Canouil
Mickaël Canouil
Head of Biostatistics

Biostatiscian, cinephile and @rlille_rug organiser.

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