I find when I write notes or try and explain how something works to someone else, I easily lose track of when some value has been "normalized", and what exactly normalization in this circumstance means.
For example, a particular ChIP-Seq assay could be:
Normalized by total reads in sample
Normalized by total signal in sample
"Normalized" to signal in input control (which generally gets normalized itself)
Quantile normalized to other samples of the same assay type
I'm sure there are other, more complicated, ways to "normalize" -- and perhaps in half the cases where I say I have normalized the data I have actually just "transformed it" (certainly the distribution is not normal) -- but those are the ones I commonly do. Given that their is so much room for ambiguity here, I was wondering if there is a standard nomenclature for this in Mathematics or Statistics? I don't think there are enough symbols for every normalization scenario - but just to be able to differentiate between input normalized, read count normalized, and not at all normalized, would really help. Googling "normalization symbol" didn't help :(
If you have any other examples of confusing terminology or non-specific "bioinformatic slang", it would be great to hear about those too :) Some times I don't realize how unspecific i'm being when i say things (usually because I expect everyone to know what I mean), so it would be great to hear common tropes people encounter or use themselves.