Exactly as Jürgen Weippert state - a good solvent extraction and filtration before chromatography is essential. Also - depending on what you are looking for you may need to extract to different solvent systems, e.g. polar and non-polar and clean these up (not just simple filtering) before analysis. Stools are a complex matrix to extract and include some lipids. You may need to dilute to be able to resolve some chemical compoents also.
There are a number of diagnostic analyses that use this technique, so looking for their methods in the literature may help get you more detailed process. Suggest look for porphyria diagnostic method via chromatography.
Thank you. I did not find anything on PubMed with `porphyria diagnostic method via chromatography` but there are too many titles on Google scholar. Would you have a title I could browse?