7.8 years ago by
Gene Set Enrichment Analysis works by ranking the "differentially" expressed genes between "two groups" and calculating a sum statistic eventually reporting a Enrichment score. As Chris pointed out if you ask a question like, "Is my set of genes are enriched in a particular cell type?", the implicit thing is you are comparing the gene set in your cell type of interest with "some" other.
As you said, if you want to find out whether your gene set is "enriched" (actually it would be misnomer to use for a single cell type), then you could just sort your list of genes based on the absolute expression values, then select a list of genes above a certain threshold (you could possibly calculate mean to guide you to select a threshold). Now you check how many genes in your list is present in the genes that are above threshold value.
lets say you have 10 genes in genelist, out of which 6 has been above your threshold value, then you could report 6/10 enriched in the cell type.
Two things you need to make sure,
(a) How do you combine the expression values of Affy and Illumina, wat strategy are you using to scale both the values in same range?
(b) What I suggested is just an idea, you have to extend that further