Thanks to provide this fantastic tool, During check the calculation code of AUC score, what puzzle me is the ranking of gene. From the vignettes file in AUCell, the highly expressed gene have higher rank value ('For each cell, the genes are ranked from highest to lowest value. The genes with same expression value are shuffled. Therefore, genes with expression ‘0’ are randomly sorted at the end of the ranking'). And it's reasonable to calculate AUC score by high rank genes in 'gene set' or regulon.
But the code 'x <- sort(x[x<aucThreshold])' in 02_calcAUC.R (line: 279) extract lower rank gene to calculate AUC score. Most lower rank genes are genes with expression ‘0’, so is there some procedure that I lost to reverse the gene ranking?
Thanks to point this out.
Hi,
Thanks to provide this fantastic tool, During check the calculation code of AUC score, what puzzle me is the ranking of gene. From the vignettes file in AUCell, the highly expressed gene have higher rank value ('For each cell, the genes are ranked from highest to lowest value. The genes with same expression value are shuffled. Therefore, genes with expression ‘0’ are randomly sorted at the end of the ranking'). And it's reasonable to calculate AUC score by high rank genes in 'gene set' or regulon. But the code 'x <- sort(x[x<aucThreshold])' in 02_calcAUC.R (line: 279) extract lower rank gene to calculate AUC score. Most lower rank genes are genes with expression ‘0’, so is there some procedure that I lost to reverse the gene ranking? Thanks to point this out.
Thanks, Bing