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Transmission spectra of exoplanets orbiting active stars suffer from wavelength-dependent effects due to stellar photospheric heterogeneity. WASP-19b, an ultra-hot Jupiter (Teq ∼ 2100 K), is one such strongly irradiated gas-giant orbiting an active solar-type star. We present optical (520–900 nm) transmission spectra of WASP-19b obtained across eight epochs, using the Gemini Multi-Object Spectrograph (GMOS) on the Gemini-South telescope. We apply our recently developed Gaussian Processes regression based method to model the transit light-curve systematics and extract the transmission spectrum at each epoch. We find that WASP-19b’s transmission spectrum is affected by stellar variability at individual epochs. We report an observed anticorrelation between the relative slopes and offsets of the spectra across all epochs. This anticorrelation is consistent with the predictions from the forward transmission models, which account for the effect of unocculted stellar spots and faculae measured previously for WASP-19. We introduce a new method to correct for this stellar variability effect at each epoch by using the observed correlation between the transmission spectral slopes and offsets. We compare our stellar variability corrected GMOS transmission spectrum with previous contradicting MOS measurements for WASP-19b and attempt to reconcile them. We also measure the amplitude and timescale of broad-band stellar variability of WASP-19 from TESS photometry, which we find to be consistent with the effect observed in GMOS spectroscopy and ground-based broad-band photometric long-term monitoring. Our results ultimately caution against combining multiepoch optical transmission spectra of exoplanets orbiting active stars before correcting each epoch for stellar variability.

Traditionally, ground-based spectrophotometric observations probing transiting exoplanet atmospheres have employed a linear map between comparison and target star light curves (e.g. via differential spectrophotometry) to correct for systematics contaminating the transit signal. As an alternative to this conventional method, we introduce a new Gaussian Processes (GP) regression-based method to analyse ground-based spectrophotometric data. Our new method allows for a generalized non-linear mapping between the target transit light curves and the time-series used to detrend them. This represents an improvement compared to previous studies because the target and comparison star fluxes are affected by different telluric and instrumental systematics, which are complex and non-linear. We apply our method to six Gemini/GMOS transits of the warm (Teq  = 990 K) Neptune HAT-P-26b. We obtain on average ∼20  per cent better transit depth precision and residual scatter on the white light curve compared to the conventional method when using the comparison star light curve as a GP regressor and ∼20  per cent worse when explicitly not using the comparison star. Ultimately, with only a cost of 30 per cent precision on the transmission spectra, our method overcomes the necessity of using comparison stars in the instrument field of view, which has been one of the limiting factors for ground-based observations of the atmospheres of exoplanets transiting bright stars. We obtain a flat transmission spectrum for HAT-P-26b in the range of 490–900 nm that can be explained by the presence of a grey opacity cloud deck, and indications of transit timing variations, both of which are consistent with previous measurements.