A substance analyzer utilizing Prompt Gamma Neutron Activation Analysis for identifying characteristics of a substance and method of manufacturing the same are disclosed. The analyzer is small enough to be portable and to allow its use in many applications where current analyzers cannot be utilized. The analyzer uses a neutron radiation source and a gamma-ray detector to activate the sample material and detect the prompt gamma rays emitted by the sample material. A novel housing for such an analyzer and method for making the housing are also described. Novel methods of operating such an analyzer including via a communications network are also disclosed. Also disclosed are data analysis methods that improve the accuracy and sensitivity of the results of such material analysis.