How does ROSALIND calculate Cell Type Profiling?

Abundance of various cell populations is calculated on ROSALIND using the Cell Type Profiling Module. The method quantifies cell populations using marker genes which are expressed stably and specifically in given cell types. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value less than or equal to 0.05. 

Currently, there is not a way to view the results that do not make the p-value cutoff on our platform. However, you could view a list of the genes and their associated cell types through the Nanostring Panel Gene Lists, which can be found on the Nanostring website here. In order to manually calculate the cell type score for any given sample, it would be the arithmetic mean of the Normalized expression values for all the genes expressed with the given cell type. More details about Cell Type Profiling Algorithm can be found on page 84 of the nCounter® Advanced Analysis 2.0 User Manual.

Below is a short tutorial on our Term Exploration/Cell Type Profiler. We include topics like how to interpret your heatmap, how to filter the list of cell types, and how to change the data display of any specific cell type. 


HubSpot Video