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This is a pseudo-intensity which is added to the median spectrum.
This is used to ensure that any division with the median spectrum will not result in a division by zero.
Indeed, one could infer the pseudo-part dynamically from the spectra. But since this only happens if the 5% quantile is 0, we considered the chances of any negative effects quite low.
Is this particular decision bringing you any negative side-effects?
I was trying to make sense of the plot_fcs function. This function was used there.
Since the 0 values were excluded from the spectrum are there any chances of receiving 0 value in any quantile?
Could you specify what you meant by 'negative side effects'
Introducing pseudo-intensities or pseudo-counts always has the problem of introducing negative side-effect, such as a lower dynamic range in any quotient, as pointed out by you. Thus, if one wants to introduce such a pseudo-intensity/count one should try to have it as low as possible in order to not mess up with this.
In this particular use-case this pseudo-intensity does not influence the chances of receiving 0 values (because it can reach 0 if the specific field in rspec is 0 :) Here, it just leads to a minimal skew (due to pseudo-intensity), but most importantly, avoid division by zero.
The code chunk can be found here.
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