About the IsoGeneGUI
The IsoGene Graphical User Interface (IsoGeneGUI) is a user friendly interface of the IsoGene package which is aimed to perform analysis of dose-response studies in microarray experiments. Additionally, the GUI contains extra methods from packages orQA, ORIClust and ORCME. The IsoGeneGUI is developed for the user with no or limited knowledge about R programming so he/she can perform the analysis of dose-response for high dimensional data as well as for data from a single experiment, but with a focus on microarray setting. This GUI was developed using tcl/tk.

The main window of the package is presented below.

Screenshot of the main IsoGeneGUI window

The GUI has six main menus and in the middle of the window there is an info box. The package has six main menus: File, Analysis(HD), Analysis(SD), Clustering, Plots and Help.

File:
      1. Open dataset
          a. R workspace (*.RData files)
          b. Excel or Text files (*.xls or *.txt files)
      2. Show dataset
      3. Exit

Analysis(HD): 
     1. Set Seed
     2. Likelihood Ratio Test (E2): Asymptotic
     3. Permutation
     4. Significant Analysis of Microarrays (SAM)
         a. SAM Permutation
         b. SAM Analysis
    5. Likelihood Ratio Test (E2): orQA
    6. GORIC

Analysis(HD): 
     1. Set Seed
     2. Likelihood Ratio Test (E2): Asymptotic
     3. Permutation
     4. GORIC
     5. IsoPlot
     6. Permutation P-values Plot

Clustering: 
     1. ORCME
    2. ORIClust

Plots:       
    1. IsoPlot
    2. Permutation P-values Plots
    3. SAM Plot
        a. Plot of FDR vs. Delta
        b. Plot of number of significant genes vs. Delta
        c. Plot of number of False Positive vs. Delta
    4. User Defined Scatter Plot
    5. Plot ORCME clusters

Help:   
  1. IsoGene Help
  2. IsoGeneGUI Help
  3. About

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