We present an analysis of Spitzer/IRAC primary transit and secondary eclipse lightcurves measured for HD209458b, using Gaussian process models to marginalise over the intrapixel sensitivity variations in the 3.6 micron and 4.5 micron channels and the ramp effect in the 5.8 micron and 8.0 micron channels. The main advantage of this approach is that we can account for a broad range of degeneracies between the planet signal and systematics without actually having to specify a deterministic functional form for the latter. Our results do not confirm a previous claim of water absorption in transmission. Instead, our results are more consistent with a featureless transmission spectrum, possibly due to a cloud deck obscuring molecular absorption bands. For the emission data, our values are not consistent with the thermal inversion in the dayside atmosphere that was originally inferred from these data. Instead, we agree with another re-analysis of these same data, which concluded a non-inverted atmosphere provides a better fit. We find that a solar-abundance clear-atmosphere model without a thermal inversion underpredicts the measured emission in the 4.5 micron channel, which may suggest the atmosphere is depleted in carbon monoxide. An acceptable fit to the emission data can be achieved by assuming that the planet radiates as an isothermal blackbody with a temperature of $1484pm 18$ K.
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