When to normalise urine using metaXCMS? May 14, 2012, 11:21:29 AM Hi,I am using metaXCMS for human urine samples where there are 3 subjects and 2 conditions (fed and unfed) with 3 replicate injections and I need to normalise appropriately to account for sample dilution between subjects. It would be good to normalise across all of the samples together to the median fold change and this would usually be following peakpicking. However if I am treating each subject individually I cannot easily do this, perhaps there is a way as I don't want any false negatives/positives. I don't know how I could do this when I am generating a diffreport seperately for each individual? I read through the nature protocols paper and could not find any suggestions on fitting in a normalisation step. I have already used metaXCMS and it is working very well and some interesting features have arisen based on monoisotopic mass but I want to ensure my interpretation is accurate. I am considering in future to normalise to osmolality and correcting each sample prior to data acquistion in future however for now does anyone have any suggestions of how I can normalise these urine samples so that I don't misintepret the second order analyses with metaXCMS and fit it into the work scheme?Also does anyone have any suggestions on how I can search my own database or the soon to be released FooDB when generating the XCMS diff report instead of/ in addition to Metlin?Thanks very much.