The SPIRE Fourier Transform Spectrometer on board the Herschel Space Observatory had two standard spectral resolution modes for science observations: high resolution (HR) and low resolution (LR), which could also be performed in sequence (H+LR). A comparison of the HR and LR resolution spectra taken in this sequential mode, revealed a systematic discrepancy in the continuum level. Analysing the data at different stages during standard pipeline processing, demonstrates the telescope and instrument emission affect HR and H+LR observations in a systematically different way. The origin of this difference is found to lie in the variation of both the telescope and instrument response functions, while it is triggered by fast variation of the instrument temperatures. As it is not possible to trace the evolution of the response functions through auxiliary housekeeping parameters, the calibration cannot be corrected analytically. Therefore an empirical correction for LR spectra has been developed, which removes the systematic noise introduced by the variation of the response functions.
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