I'm in the process of project shopping, but at the moment am starting to  look at noise properties in the Lyman alpha forest. The goal is to  quantify the effects of various components of noise on the power  spectrum, P(k), derived from the Ly-alpha forest.
Although the results  of the power spectrum are dependent on many physical properties (such as  whether to include or how to deal with Damped Lyman Alpha systems,  velocity broadening, metal-line systems, and continuum fitting), I plan  to study the effects due to the data itself. Namely, four components add  sufficient noise to affect our results.
1) Measurement noise --  read, sky & object noise (Poisson)
2) Sky-subtraction
3)  Spectro-photometry -- effects due to the amount of light entering the  fiber based on position on plate (?), which would largely affect the  continuum fits of the Ly-A forest
4) Wavelength calibration
Not  sure if this is correct, but it seems as though spectro-photometry and  sky subtraction would cause the biggest source of error. The first test  I'll conduct will be the effects of sky subtraction. I'll use the mock  catalog which has 'perfect' data, unaffected by noise, and add only that  noise due to sky subtraction. The mock catalog is made such that to  emulate the BOSS survey (while simultaneously made with the correct  distribution to give the correct power spectrum), so I'll use sky  spectra from fibers closest (in ra/dec) to our mock spectra. After  adding sky subtraction noise, I'll compute the correlation function on  the sample to see how it deviates from the ideal case.