Modifications were made to the Sloan Digital Sky Surveys Baryonic Oscillations Spectroscopic Survey (SDSS/BOSS) optical fibres assigned to quasar targets in order to improve the signal-to-noise ratio in the Lyman-alpha forest. However, the penalty for these modifications is that quasars observed in this way require additional flux correction procedures in order to recover the correct spectral shapes. In this paper we describe such a procedure, based on the geometry of the problem and other observational parameters. Applying several correction methods to four SDSS quasars with multiple observations permits a detailed check on the relative performances of the different flux correction procedures. We contrast our method (which takes into account a wavelength dependent seeing profile) with the BOSS pipeline approach (which does not). Our results provide independent confirmation that the geometric approach employed in the SDSS pipeline works well, although with room for improvement. By separating the contributions from four effects we are able to quantify their relative importance. Most importantly, we demonstrate that wavelength dependence has a significant impact on the derived spectral shapes and thus should not be ignored.
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