Hi,

   I have been using ABA enrichment analysis and I need some help in using the quantile cut-off value for enrichment analysis of my dataset (19 genes) using hypergeometric test. How is the quantile cut-off value selected, is it based on the expression dataset? I read in the vignette that quantile cut-off value of 0.4  means the lowest 40% of gene expression are 'not expressed' and the upper 60% are 'expressed' for a quantile of 0.4 means the lowest 40% of gene expression are 'not expressed' and the upper 60% are 'expressed' for a quantile of 0.4. So if use 0.6 as cut-off value does it mean, the lowest 60% of gene expression are not expressed and the upper 40 % is expressed?. Since, I don't have good background in statistics,I need help in selecting the quantile cut-off value for my dataset of 19 genes or please provide some links or resources from which I can get some leads. Thanking you

Regards

Priya