Poisson noise in transmission data can have a significant influence on the statistical uncertainty of PET measurements, particularly at low transmission count rates. In this paper, we investigate the effect of transmission data processing on noise and quantitative accuracy of reconstructed PET images. Differences in spatial resolution between emission and transmission measurements due to transmission data smoothing are shown to have a significant influence on quantitative accuracy and can lead to artifacts in the reconstructed image. In addition, the noise suppression of this technique is insufficient to greatly reduce transmission scan times. Based on these findings, improved strategies for processing count-limited transmission data have been developed, including a method using segmentation of attenuation images. Using this method, accurate attenuation correction can be performed using transmission scan times as low as 2 min without increasing noise in reconstructed PET images.