We have developed two independent methods to measure the one-dimensional power spectrum of the transmitted flux in the Lyman-$alpha$ forest. The first method is based on a Fourier transform, and the second on a maximum likelihood estimator. The two methods are independent and have different systematic uncertainties. The determination of the noise level in the data spectra was subject to a novel treatment, because of its significant impact on the derived power spectrum. We applied the two methods to 13,821 quasar spectra from SDSS-III/BOSS DR9 selected from a larger sample of over 60,000 spectra on the basis of their high quality, large signal-to-noise ratio, and good spectral resolution. The power spectra measured using either approach are in good agreement over all twelve redshift bins from $<z> = 2.2$ to $<z> = 4.4$, and scales from 0.001 $rm(km/s)^{-1}$ to $0.02 rm(km/s)^{-1}$. We determine the methodological and instrumental systematic uncertainties of our measurements. We provide a preliminary cosmological interpretation of our measurements using available hydrodynamical simulations. The improvement in precision over previously published results from SDSS is a factor 2--3 for constraints on relevant cosmological parameters. For a $Lambda$CDM model and using a constraint on $H_0$ that encompasses measurements based on the local distance ladder and on CMB anisotropies, we infer $sigma_8 =0.83pm0.03$ and $n_s= 0.97pm0.02$ based on ion{H}{i} absorption in the range $2.1<z<3.7$.
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