-> sigma(A) = sqrt (sigma(My_signal)^2-sigma(N)^2))
That is a correct formula. It's your general conception of the problem that needs improvement.
For a "random variable" X , the terms "standard deviation" can have several different meanings. Among these are
1. "Standard deviation" can refer to the standard deviation as a parameter of the probability distribution for X. This type of standard deviation can be called "the population standard deviation".
2. "Standard deviation" can refer to a number (like 0.43) that you calculate from a set of data for X, in which case it should be called a "sample standard deviation".
3. Both "standard deviation" and "sample standard deviation" can refer to a formula you use to calculate the "sample standard deviation" (rather than referring to just one specific number). From this point of view, the "sample standard deviation" becomes a random variable also since it depends on random outcomes.
4. "Standard deviation" can refer to an estimate (like 0.43) of the "population standard deviation" (usually an estimate that is based on a particular sample of data). There are are a variety of ways to make estimates. There is no law that says you can only use the "sample standard deviation" as your estimate of the the "population standard deviation".
5. "Standard deviation" can refer to a formula or algorithm for making an estimate of the "population standard deviation" as a function of the data. This is called an "estimator of the standard deviation" and such an estimator is a random variable since the data is random.
There is no law that says than an estimate or an estimator must use the same formula as the formula for the population standard deviation. In fact, that would be impossible since the formula for the "population standard deviation" uses inputs that are probabilities and a formula for estimating the standard deviation must use inputs that are data values. The data might involve observed frequencies of values, but observed frequencies are not the same as probabilities. (Think of tossing a fair coin an odd number of times. The fraction of heads can't turn out to be 1/2.)
The formula you gave is correct for 1) if the signal and noise are independent random variables.
if you talk about specific numbers from an experiment, your talking about 2) or 4). If you are discussing general statistical concepts, you usually refer to 1), 3) or 5). If you have lots of data, It is likely that the formula you gave is useful for 2),3),4),5) also.
A further complication of your problem is that you have a variable sample rate. If you have a random variable X that varies continuously in time, you probably won't get the same standard deviation ( in any sense of that phrase) if you change sample rates. If you want to talk about "the" standard deviation of the random variable X, you must make an even more specialized definitions of "standard deviation" that doesn't depend on the particular sample rate. The basic idea is that the definition must incorporate the concept of "per unit time". This is why chiro suggests you look at the theory of Brownian motion.
If you use only 1 sample rate in your experiments, then the formula you gave is OK.