Cell Type Profiling methods for Nanostring nCounter Gene Expression data

Abundance of various cell types is estimated using the Cell Type Profiling algorithm developed by the NanoString Bioinformatics team. The NanoString Bioinformatics Team has identified signatures of marker genes that can be used to quantify the relative abundance of different cell types across samples. For each cell type, ROSALIND performs a dynamic selection to identify the subset of signature marker genes that are robust. The method quantifies a given cell population using marker genes that are expressed stably and specifically in given cell types. The score for Cell Type in any given sample is calculated as the arithmetic mean of the log2-transformed normalized expression of all selected marker genes for the Cell Type. More details about the Cell Type Profiling Algorithm and QC p-value calculations can be found on pages 84-86 of the nCounter® Advanced Analysis 2.0 User Manual.

*Note: prior to February 6, 2024 ROSALIND performed a filtering of Cell Type Profiling results to include results that have scores with a p-Value less than or equal to 0.05. The results that did not make the p-value cutoff on our platform are not directly available to view. 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.