It has been suggested by my platform that I normalise my mass spec metabolite data by median. Is this necessary, and what is the purpose of this type of normalisation in the context of mass spec. My concern is that this means I cannot compare between metabolites, only within metabolites.
Dear Ashlee
No, it is not always necessary. There are different normalization strategies, and the selection depends on multiple factors. However, even without normalization, your concern will not disappear. I do not know details of your experiment and data, but generally speaking you usually can compare abundances of different metabolites within a single sample after building calibration curve for these metabolites, because there are again multiple factors that affect intensity of the signal, not only the real concentration of a compound.
As stated by Albert, it is not always necessary. It depends on the type of data you obtained and on the goal of your research.
Can you be more precise and add some more details regarding your experiment in your question?
It is depends on data but it is better to normalize wherever it is applicable.
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