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XCMS - FAQ / Why can you not compare multiple cases to a single control in XCMS?
Something that I have noticed when I process my own data in a case control manner is that I get aligned peak tables (assuming I processes the data once for each of my two cases) with more unique features from the two peak tables than the peak table I get when I process my data using both cases and the same control. There are equivalent number of replicates of each case and the control. I know xcms is meant to be run in a case/control fashion, but does anyone know why I might observe this difference in the number of unique features?
Just to clarify a few things, I have used peak picking parameters that have been optimized to our instrument and the raw data. For the most part, they are similar. I have also set classes with respect to each experimental case, and set the retention time correction parameters to account for the appropriate number of samples that may be missing due to the fact that they are in only one treatment and not the other.
I would be very grateful if anyone had any knowledge of how these algorithms work so I could improve my ability to use them.