Considering Ly-forest in spectra of quasars one speaks about the transmitted flux which is given by
where is the continuum, is the transmission and is the opacity or optical depth. For the spectrum reduced by the continuum fitting:
where describes the stochastic noise (including the Poisson noise of the photon count). Averaging over the density fluctuations (over all the pixels in a certain redshift bin) one can obtain: , which is called mean transmitted flux. Generally speaking, this value is position dependent, as it depends on the photoionization rate of HI and the temperature of the intergalactic medium.