Help

How to ?

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How to Use Data Analysis Wizard?

Step 1

Please click on the Data Analysis Wizard at the top green menu in the home page as shown in the following example.


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Step 1 - Option 2

One can also use the data analysis wizard from the browse functionality area as shown in the example below.Skip to step 3.


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Step 1 - Option 3

One can also use the data analysis wizard from after searching for a gene and clicking the "Data Analysis" button as shown in the example below.Skip to Step 3.


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Step 2

The resulting page from Step1 - option 1 will be like the following example. Please select an experiment as shown below.


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Step 3

Please select a platform as shown below and click the submit button.


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Step 4

Please select the Genotypes that you want to compare as shown in the example.


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Step 5

The wizard will create a data file now with the selected data from Step 1 to Step4 .Please provide a missing value imputation threshhold. This is a required step and the the data wizard will not proceed further unless user makes data preprocessing choices at this step. Please read the description of the algorithm at the left side of the wizard.An example is shown below:


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Step 6

The wizard will now ask for the Normalization method.Please select a data normalization method. This is a required step and the the data wizard will not proceed further unless user makes data preprocessing choices at this step. Please read the description of the algorithm at the left side of the wizard. An example is shown below:


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Step 7

After completing the required pre processing steps, the users can select any of the multivariate methods described below for data analysis.

Step 7: Option 1 - Hierarchical Clustering

Please make choices for Linkage method and distance measure from the drop down list and press the submit button to generate hierarchical clustering plots. Please read the description of the algorithm by clicking at the Help icon at the left side of the wizard. Please click on the sample plot above the generated plot to get help on interpretation of the plot. An example is shown below:


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Step 7: Option 2 - MDS Clustering

Please make choices for distance measure from the drop down list and press the submit button to generate MDS clustering plots. Please read the description of the algorithm by clicking at the Help icon at the left side of the wizard. Please click on the sample plot above the generated plot to get help on interpretation of the plot. An example is shown below:


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Step 7: Option 2 - PCA Analysis

Please press the submit button to generate PCA loadings plot for the first 2 PCs. Please read the description of the algorithm by clicking at the Help icon at the left side of the wizard. Please click on the sample plot above the generated plot to get help on interpretation of the plot. An example is shown below:


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Step 7: Option 2 - Random Forest Analysis

Please press the submit button to generate Random Forest analysis. Please read the description of the algorithm by clicking at the Help icon at the left side of the wizard. Please click on the sample plot above the generated plot to get help on interpretation of the plot. An example is shown below:


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Step 8

All the outputs are made available for download at the end as shown in the example below.


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