I'm reading [this fantastic article on estimating body time: Molecular-timetable methods for detection of body
time and rhythm disorders from single-time-point
genome-wide expression profiles](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509173/pdf/10111227.pdf) and one of the things that is not very clear to me is how the researchers estimated which genes are expressed and which ones are not:

> 
> Total RNA was prepared by using Trizol reagent (GIBCOBRL). cDNA
>  synthesis and cRNA labeling reactions were performed as described (5).
>  Affymetrix high- density oligonucleotide arrays (Murine Genome Array
>  U74A, Version 1.0, measuring 9,977 independent transcripts) were
>  hybridized, stained, and washed according to the Technical Manual
>  (Affymetrix). Affymetrix software was used to deter- mine the average
>  difference (AD) between perfectly matched probes and
>  single-base-pair-mismatched probes. The AD of each probe was then
>  scaled globally so that the total AD of each microarray was equal. **The
>  resulting AD values reflect the abundance of a given mRNA relative to
>  the total RNA popu- lation and were used in all subsequent analyses**
> 
> 
> 

I'm not sure if I'm reading this correctly - did the researchers look at all RNA available in the cells and calculated the levels of messenger RNA produced by expressed genes? if not, how can the level of expression of a gene be estimated?