2024 | Jarosław Chilimoniuk, Anna Erol, Stefan Rödiger, Michal Burdukiewicz
The article "Challenges and Opportunities in Processing NanoString nCounter Data" by Jarosław Chilimoniuk, Anna Erol, Stefan Rödiger, and Michal Burdukiewicz reviews the NanoString nCounter technology, a medium-throughput platform used for mRNA and miRNA differential expression studies. The authors highlight the platform's advantages, such as the absence of an amplification step and its ability to analyze low-grade samples, but note that its popularity has stabilized in recent years, possibly due to the lack of standardized analytical pipelines. To address this, they outline a standardized workflow consisting of five steps: data pre-processing, quality control, background correction, normalization, and differential expression analysis.
The article evaluates eleven R packages designed for nCounter data processing, categorizing their functionalities and discussing their applications in mRNA and miRNA studies. It emphasizes the importance of accurate background correction, normalization, and differential expression analysis to ensure reliable results. The authors recommend using NanoTube for mRNA data analysis due to its robustness and user-friendly graphical user interface (GUI), while nSolver is suggested for miRNA data processing due to its support for ligation control normalization. RCRdiff is highlighted as the only method for differential expression analysis that does not require normalization.
The conclusion underscores the importance of selecting appropriate analytical methodologies to ensure the robustness and reliability of data obtained from the nCounter platform. The authors provide a comprehensive overview of the nCounter data processing workflow and the available tools, aiming to facilitate the comparison and selection of suitable methods for different research needs.The article "Challenges and Opportunities in Processing NanoString nCounter Data" by Jarosław Chilimoniuk, Anna Erol, Stefan Rödiger, and Michal Burdukiewicz reviews the NanoString nCounter technology, a medium-throughput platform used for mRNA and miRNA differential expression studies. The authors highlight the platform's advantages, such as the absence of an amplification step and its ability to analyze low-grade samples, but note that its popularity has stabilized in recent years, possibly due to the lack of standardized analytical pipelines. To address this, they outline a standardized workflow consisting of five steps: data pre-processing, quality control, background correction, normalization, and differential expression analysis.
The article evaluates eleven R packages designed for nCounter data processing, categorizing their functionalities and discussing their applications in mRNA and miRNA studies. It emphasizes the importance of accurate background correction, normalization, and differential expression analysis to ensure reliable results. The authors recommend using NanoTube for mRNA data analysis due to its robustness and user-friendly graphical user interface (GUI), while nSolver is suggested for miRNA data processing due to its support for ligation control normalization. RCRdiff is highlighted as the only method for differential expression analysis that does not require normalization.
The conclusion underscores the importance of selecting appropriate analytical methodologies to ensure the robustness and reliability of data obtained from the nCounter platform. The authors provide a comprehensive overview of the nCounter data processing workflow and the available tools, aiming to facilitate the comparison and selection of suitable methods for different research needs.