Hey cool SC3-developers, I have a question about marker genes and normal genes. As I understood, marker genes are highly expressed genes in one cluster and have abilities (filtered by padj, ROC) to distinguish this cluster between others.   Concerning normal genes that cannot pass the threshold in the same cluster, how could we explain about them? Some of them are neither marker genes nor differentially expressed genes of that cluster, why are they assigned to that specific cluster??? Thank you very much and, looking forward to your reply. :)

Hi, I would recommend you to read more about receiver operating characteristic (https://en.wikipedia.org/wiki/Receiver_operating_characteristic). Genes in which area under the ROC curve is less than the threshold are closer to completely random guess than the ones above the threshold. If you reduce the threshold they will be included in the list of marker genes, but will be weak representers of their cluster. However, when the area under the ROC curve is 0.5, it means that these genes are no better than a random guess.