An improved measurement of the flux distribution of the Ly-alpha forest in QSO absorption spectra: the effect of continuum fitting, metal contamination and noise properties

We have performed an extensive Voigt profile analysis of the neutral hydrogen (HI) and metal absorption present in a sample of 18 high resolution, high signal-to-noise QSO spectra observed with VLT/UVES. We use this analysis to separate the metal contribution from the HI absorption and present an improved measurement of the flux probability distribution function (PDF) due to HI absorption alone at <z> = 2.07, 2.52, and 2.94. The flux PDF is sensitive to the continuum fit in the normalised flux range 0.8 < F < 1.0 and to metal absorption at 0.2 < F < 0.8. Our new measurements of the flux PDF due to HI absorption alone are systematically lower at 0.2 < F < 0.8 by up to 30% compared to the widely used measurement of McDonald et al. (2000), based on a significantly smaller sample of Keck/HIRES data. This discrepancy is probably due to a combination of our improved removal of the metal absorption and cosmic variance, since variations in the flux PDF between different lines-of-sight are large. The HI effective optical depth at 1.7 < z < 4 is best fit with a single power law, (0.0023 +-0.0007) (1+z)^(3.65 +- 0.21), in good agreement with previous measurements from comparable data. As also found previously, the effect of noise on the flux distribution is not significant in high resolution, high signal-to-noise data.