I am currently using the MaldiQuant package in R for the pre-processing of mass spectra data. When I apply the median normalization to some of my datasets with the following line: spectra <- calibrateIntensity(spectra, method = "median") , I receive the following warning:

Warning messages: 1: In fun(object@intensity, ...) : Scaling factor is zero. No calibration applied.

I was wondering if this is anything to worry about? I have at least 3 biological replicates per sample, and for some replicates for a specific m/z value the intensity before normalization is actually 0, so I am thinking that this warning message simply indicates that no scaling can be done to these specific values. Is this the correct way of interpreting the warning message?

Thanks very much for any help!