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Visual Comparison of Hybridizations & Treatments


   Step 1. Select experiments:

        X-axis of Scatterplots:
        
        Y-axis of Scatterplots:
        
            *X- and Y- axes can be from different experiments, which must be of same GeneChip type

   Step 2. Select expression estimation method:

        


   Step 3. Select a Visualization Method:    Help 


1. Scatter Plot & MvA Plot for Treatment Means

     Showing data distribution and expression variability between treatments.
    
     Treatment for x-axis: 
     Treatment for y-axis: 
 
    
 

2. Scatter Plot & MvA Plot for Individual Hybridizations    
     Showing data distribution and expression variability between hybridizations.
    
     Hybridization for x-axis: 
     Hybridization for y-axis: 
 
    
 

3. M vs. A Plots Matrix for Replicates of a Treatment
     Showing the reproducibility among replicate hybridizations

     Select a Treatment:        
 
    
 

4. M vs. A Plots Matrix for Selected Hybridizations
     Showing the variability among selected hybridizations

     Select Up to 6 Hybridizations from Column 1 of Table Below (1 to 4 minutes for 3 to 6 hybridizations):
    
 


     Plot Scale:Log2 Scale(recommended)Original Linear Scale. (RMA estimation values are by default in log2 scale.)


Information of Hybridizations from BB1 

HybridizationTREPFactor:
species
File_NameSample_ID & Name
1 BB1_H111Barley0308-6BB1_S1
Expt# 11666-10
2 BB1_H212Barley0315-6BB1_S2
Expt # 11771-6
3 BB1_H321Wheat0308-1BB1_S3
Expt# 11666-1
4 BB1_H422Wheat0315-5BB1_S4
Expt# 11771-5
5 BB1_H531Oat0308-5BB1_S5
Expt# 11666-8
6 BB1_H632Oat0315-4BB1_S6
Expt# 11771-4
7 BB1_H741Sorghum0308-3BB1_S7
Expt# 11666-5
8 BB1_H842Sorghum0315-2BB1_S8
Expt # 11771-2
9 BB1_H951Corn0308-4BB1_S9
Expt# 11666-7
10 BB1_H1052Corn0315-3BB1_S10
Expt# 11771-3
11 BB1_H1161Rice0308-2BB1_S11
Expt# 11666-2
12 BB1_H1262Rice0315-1BB1_S12
Expt # 11771-1
T= Treatment; REP = Replicate
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