The hot Jupiter HD 209458b was observed during primary transit at 3.6, 4.5, 5.8 and 8.0 microns using the Infrared Array Camera (IRAC) on the Spitzer Space Telescope. We detail here the procedures we adopted to correct for the systematic trends present in the IRAC data. The light curves were fitted including limb darkening effects and fitted using Markov Chain Monte Carlo and prayer-bead Monte Carlo techniques, finding almost identical results. The final depth measurements obtained by a combined Markov Chain Monte Carlo fit are at 3.6 microns, 1.469 +- 0.013 % and 1.448 +- 0.013 %; at 4.5 microns, 1.478 +- 0.017 % ; at 5.8 microns, 1.549 +- 0.015 % and at 8.0 microns 1.535 +- 0.011 %. Our results clearly indicate the presence of water in the planetary atmosphere. Our broad band photometric measurements with IRAC prevent us from determining the additional presence of other other molecules such as CO, CO2 and methane for which spectroscopy is needed. While water vapour with a mixing ratio of 10^-4-10^-3 combined with thermal profiles retrieved from the day-side may provide a very good fit to our observations, this data set alone is unable to resolve completely the degeneracy between water abundance and atmospheric thermal profile.
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