Considering Ly$\alpha$-forest in spectra of quasars one speaks about the transmitted flux which is given by where $F_{cont}(\lambda )$ is the continuum, $e^{-\tau }$ is the transmission and $\tau (\lambda )$ is the opacity or optical depth. For the spectrum reduced by the continuum fitting: where $n(\lambda )$ describes the stochastic noise (including the Poisson noise of the photon count). Averaging $F(\lambda )$ over the density fluctuations (over all the pixels in a certain redshift bin) one can obtain: $\bar {F}(\lambda )=\left \langle e^{-\tau (\lambda )}\right \rangle$, 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.