I want to identify tissue specific genes
I have 2 data sets:
Set 1) RPKM values for all gene in the tissue of interest
Set 2) RPKM values for all genes of many other tissue types
Should I choose a low RPKM cutoff for the genes in the tissue of interest? If so, how do I choose the cutoff?
I have 2 concerns:
A) If I dont choose a cuttoff then any expression (no matter how small) in the tissue that is not found in other tissues indicates tissue specificity For example: RPKM values for gene X in set 1 is 1.0 and in set 2 is 0.0 - Would it be a mistake to say gene X is is tissue specific?
B) If I do choose a cutoff am I incorrectly excluding rarely expressed genes? For example: A cutoff RPKM value of 2.0 would exclude gene X above.
Thanks in advance. Kenneth.