threshold

[alperyilmaz]

In Mortazavi et al (Nature Methods,2008. 5: 621) they used 5 RPMK as threshold and reported genes that had RPMK more than 5.0.
Is this applicable to other experiments or this threshold can be applied to certain experimental values (number of reads, genome size, etc.)?
If 5.0 is not applicable to other experiments, how can I calculate for my particular experiment?

thanks..

[steven]

i would take a look at the distribution of all RPKM values before setting any threshold