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)

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Define the Treatments to be Included in Analysis

    Factor1: 1. All Levels of factor genotype2. Wheat (BB1-H1/S1)3. Barley (Mla1-5874-0hai)

Experiment Design Details:

Hybridization	T	REP	Factor: genotype	File_Name	Sample_ID & Name
1 TA1_H1	1	1	Wheat (BB1-H1/S1)	0502-1_0308-1_BB1_H3_Wheat	TA1_S1 0308-1
2 TA1_H2	2	1	Barley (Mla1-5874-0hai)	0502-2_0449-35	TA1_S2 0449-35
T= Treatment; REP = Replicate