How do you calculate and define the average expression of the gene, especially in the context of the plotting of genes in dot plots? What does it mean when the average expression is <0?
In Cellenics, we are using the DotPlot function from the Seurat R package, so the average expression of a gene is calculated across a specific cluster or group of cells. This function uses the scaled data, where the data is standardized to have a mean of 0 and a standard deviation of 1. In this context, if the average expression is less than 0, it means that the gene’s expression in that specific group is below the mean expression across the entire dataset. This scaling approach helps to visualize both lowly expressing clusters and highly expressing clusters on the same scale. So, a negative value doesn’t mean the gene has a “negative expression” in a biological sense. Instead, it indicates that the gene is underexpressed in that group compared to the overall mean expression of the dataset.
I hope this helps. If you have any more questions or need further clarification, please don’t hesitate to ask!