The effect of JWST/NIRSpec data reduction on the retrieval of WASP-39b atmospheric properties

Context . The James Webb Space Telescope (JWST) provides exoplanetary transit observations with an unprecedented spectral range coverage, offering exceptional data on exoplanet atmospheres. Nevertheless, the presence of systematics in the data reduction process introduces small, but significant uncertainties that propagate into atmospheric retrievals. Understanding how these reduction choices affect interpreted atmospheric properties is essential. Aims . We aim to quantify the impact of different JWST/NIRSpec PRISM data-reduction processes, as well as the relevance of saturation on the retrieved atmospheric properties of WASP-39b. We also assess whether or not these biases are comparable to those introduced by assumptions made in atmospheric modelling, particularly in the treatment of aerosol extinction. Compared with previous similar efforts, we use the highest number of alternative data reductions and discuss the role of the saturated spectral region, without adding any additional data from other sources or random noise, in contrast to previous works. Methods . We performed a series of nested-sampling Bayesian retrievals using MultiNest and forward models generated with the Planetary Spectrum Generator. We analysed six independently reduced NIRSpec/PRISM spectra and compare retrievals using the full wavelength range as well as versions excluding the saturated 0.69-1.91 μm region. We further tested the effect of including three different cloud-opacity parametrisations. Results . Significant discrepancies arise among retrievals based on different calibrations, affecting key atmospheric parameters such as temperature, molecular abundances, and cloud opacity, often at a level exceeding one order of magnitude. Excluding the saturated region reduces the inter-pipeline dispersion; conversely, however, it also increases degeneracies between parameters. Differences introduced by data reduction are comparable in magnitude to those produced by distinct cloud-opacity models. Bayesian evidence systematically favours non-flat aerosol extinction, although the preferred spectral behaviour depends on the specific calibration used. Conclusions . Variations among JWST/NIRSpec data-reduction pipelines produce measurable and often substantial differences in retrieved atmospheric properties of WASP-39b. These biases are similar in scale to the uncertainties on modelling assumptions, underscoring the importance of robust and homogeneous calibration procedures. The results also confirm that JWST data possess the sensitivity required to probe aerosol spectral behaviour, although such constraints remain strongly dependent on the adopted data-reduction strategy.