Step 1. Choose a Gene List for Analysis: Gene List Management 

Step 2. Select an Analysis Method from the List: 

Step 3. Setup Analysis and Run: 

Log2 transform data if not yet, for example the MAS5.0 estimations.
Mean-center log2 transformed data so that each row has mean 0.

Select a clustering method:
single linkage average linkage complete linkage ward mcquitty median centroid
Select a distance method:
Correlation - Centered Pearson Non-Centered Pearson Euclidean Distance maximum manhattan canberra
     The number of clusters to use (may based on preliminary output) is  

Heapmap color spectrum: Green (low) and Red (high)  Blue (low) and Yellow (high)

---

Define the Treatments to be Included in Analysis

    Factor1: 1. All Levels of factor genotype2. Fgh Butte 863. Water (mock)
    Factor2: 1. All Levels of factor time2. 24 hai3. 48 hai4. 72 hai5. 96 hai6. 144 hai

Experiment Design Details:

Hybridization	T	REP	Factor: genotype	Factor: time	File_Name	Sample_ID & Name
T= Treatment; REP = Replicate