Hello rteich;
First-order effects of heat sink performance versus ambient can generally be ignored. If you're talking about, 32° F. versus 90° F. then yes ambient should probably be taken into consideration. What I'm led to believe, with regards to your case, is you're just doing tests on possibly different days and the local ambient is subject to being several degrees different.
Understand that your heat sinks are using two techniques for ridding themselves of heat. One is radiation the other is convection (fan driven though it may be). If your design is heavily dependent on radiation then the ambient makes a much larger difference and will possibly even be a first-order effect. If air circulation is fan forced then radiation will likely be a second order effect.
Most heatsink studies aren't worried about low temperature operation as the high-temperature operation will be the thing causing the product a problem.
So yes, if you are making comparisons between different heat sinks in the the same approximate ambient, plotting the difference between a data point and ambient for each set of data will exclude your ambient temperature from your testing. Keeping in mind what I said previously!
If you're running fan forced air across your heat sinks, the radiation component is pretty much overridden.
By wind, I meant if you're running a fan forced system or a non fan pure convection system and it's out in the open or in a breezy area those breezes will make a large difference in the performance of the heat removal system and so would have to be taken into account.
Keith Cress
Flamin Systems, Inc.-