Real time results and gene expression pattern analysis

I have a problem thinking on a paper discussion. When sb extracts RNA from a pool of embryos of different stages to analyze pattern expression of one gene: the number of cells impact in the quantity of this gene!? I mean, if there are differences in relative expression of the gene it could be due to differences in the number of cells, and not because of one cell have actually difference RNA content of this gene!? or it is not important because we work with exaclty the same RNA content to make c-DNA? I mean for example 1ug!