This thesis examines some of the challenges involved with using FTIR spectroscopy for cancer detection including sample preparation and correcting for distortion from cell scattering. Sample preparation affects the spectra differently depending on the cell type, and can lead to significant changes in cancer biomarkers for a given cell type. Biomarkers derived from specific cancer types under one sample preparation are not reliable for other cancer types, and may not be suitable for the same cancer type using a different sample preparation. Cell scattering can also significantly affect the cell spectra, and as a result, correcting for the cell scattering distortion leads to changes in the biomarkers. For reliable cancer detection controlling variability is critical, especially in the complex spectra of biological samples. Standard sample preparation methods and scattering correction post-processing could improve comparison of cancer detection methods.