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Setup Data Analysis Parameters

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: 

1. Hierarchical Clustering Settings: Help

First, decide if do clustering.
 Hierarchical Clustering:
     Cluster filtered genes      Cluster samples with filtered genes
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:

Select a distance method:

     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


Experiment Design Details:
File_NameSample_ID & Name
1 TA1_H1 11Wheat (BB1-H1/S1)0502-1_0308-1_BB1_H3_WheatTA1_S1
2 TA1_H2 21Barley (Mla1-5874-0hai)0502-2_0449-35TA1_S2
T= Treatment; REP = Replicate


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