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I'm using an Arduino Uno R3 along with an Ethernet shield as well as the linker base shield for interfacing with three linker modules, light, temperature and some LEDs as I believed this would be simpler than using a breadboard and look neater. Are there any problems I'm likely to run into regarding compatibility or power consumption? It's a prototype for a hydroponic garden automation system. As a secondary, are there any c02 sensors under $60 available on the market?

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I would recommend looking up the power consumption specs on the datasheets for each shield. Then determine whether the current used by all of the shields exceeds the limits for any given pin and for the board as a whole. I highly recommend the following article: http://www.ruggedcircuits.com/10-ways-to-destroy-an-arduino/

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