Thesis timeline and technical challenges

Well, after talking to Loren (my Major Prof), I feel that I am on track for completing my thesis in an acceptable time frame (completion in spring/summer). I have had my INAA (Instrumental Neutron Activation Analysis) data for several weeks now, and hope to have it processed by the end of next week. I am currently looking at bivariate plot groupings (element1/element2) and cluster diagrams.

One of my big questions is what to do when INAA returns back below detection limit values. These values look like negative values within my dataset. It appears that I have three options when I encounter samples with below concentration values.

Do I:

1. Throw away the element in question for all samples (if several samples have below concentration values for Sc for example, then just don't include Sc in my analysis).
   
2. Set the below detection limits results to 0, and the rest of the values to 1 for a given element.
3. Set the below detection limits results to 0, and don't touch the other values for a given element.

There's a lot more I could talk about here, but I will leave that for a later discussion.