Handling of loop design microarray experiments

### New Issue Checklist
- [x] The title is short and descriptive
- [x] The issue contains an:
- [x] Idea (new feature, user story, etc)
- [ ] Problem
- [x] You have explained the:
- [x] Context
- [x] Problem or idea
- [x] Solution or next step

### Context

A loop design (see the discussion around Fig 3 [here](https://discover.nci.nih.gov/microarrayAnalysis/Experimental.Design.jsp)) is a type of experimental design for two-color microarray experiments where each sample is labeled with both dyes and samples are directly compared to one another.

### Problem or idea

Loop designs have different considerations from reference designs. We ultimately might want to handle them differently.

### Solution or next step

It is okay to process these as single samples initially (with `SCAN::SCAN_TwoColor`, see #87). It will be an open research question to go back and see if we can improve upon this.

Start by reviewing the linked explanation of loop designs and the issue's reference to SCAN::SCAN_TwoColor. Compare the stated initial single-sample processing with the different considerations for loop and reference designs. The issue does not define a concrete implementation or completion criterion, so the desired handling remains an open research question.

Written by the indexing model from the issue text.