Can I use one waveform to subtract from the other one in labview?

Here is the thing.
I am using DAQ to aquire amplified signal to measure its noise of output.However DAQ would contribute a little noise to the whole system.My thinking is to capture two waveforms of noise from DAQ itself and the whole system(amplified circuit and DAQ) and then make the subtration calculation between them.Is it possible to make it with labview?How?
Or can I aquire two groups of signal using DAQ at the same time? If it can't be realised is there some other way?
Thanks

If I'm reading you right I don't think your original concept is valid.  If you have already done a good job with wiring, shielding, etc.  You won't be able to simply subtract a data collection of "just noise" from a collection of "noise plus signal" and expect the noise to cancel itself out.  It's random.  A better method would be to collect the same signal several times and then average the results.  Even that will only reduce repetitive components in the noise.
As smercurio said however, the most important consideration is to make sure your connection method, grounding, shielding, timing, etc is top notch to prevent noise from contaminating the signal in the first place.  I generally use differential signals through good quality twisted pairs with the shield connected on the DAQ side only (to prevent ground loops).
Using LabVIEW: 7.1.1, 8.5.1 & 2013

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