Optical coherence tomography (OCT) images of the retina are inevitably affected by the finite width of the coherence function and noise. To make low-reflective layers visible, the raw OCT signal is log transformed; to reduce the effect of noise the images can be low-pass filtered. We determined the effects of these operations on layer thickness assessment, as a function of signal-to-noise ratio (SNR), by performing measurements in a phantom eye and modeling. The log transform appeared to be the key factor in a SNR-dependent overestimation of peak widths and a less predictive bias in the widths of low-reflective layers. (C) 2016 Optical Society of America