basal gene expression level

Question

[Francois Piumi]

Hi,

Scientists are interested in differentially expressed genes but also sometimes into basal gene expression levels.

Is it possible to determine these expression levels by using read counts from a RNA-Seq count table? if yes, is there an existing rule or threshold from which we can we that a gene is expressed or not?

Answer 1

[LChart]

I haven't seen any reliable way to estimate absolute RNA concentrations from sequencing data. Methods have been developed using housekeeping genes (which are assumed to be of largely constant expression -- though this may not be the same thing as molarity) or spike-in controls. The commentary here: https://support.bioconductor.org/p/88413/ is always worth a read.