CoV-HiPathia

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====== Worked example Prediction - Train ======

  - Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]].
  - We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links:

    * Expression matrix: {{:brca_genes_vals_bn.txt|}}
    * Experimental design: {{:brca_normal-basal_ed.txt|}}

  - Upload the data to HiPathia in the data panel by clicking on //My data//. For further information on this step visit [[upload_your_data|Upload your data]].
  - Press the //Prediction// button. 

{{ :hipathia_bar_pred.png?600 |}}

  - In the //Type// panel select //Train new model//.

  - In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file.

{{ :hipathia_work1.png?600 |}}

  - In the //Design data// panel select //Two group comparison//. Press the //File browser// of the //Experimental design file//, and select the desired file. Automatically //Condition 1// and //Condition 2// files are selected. Change //Condition 1// to "Tumor" and //Condition 2// to "Normal".

{{ :hipathia_work2.png?600 |}}

  - Select Human as species (by default).
  - In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//.
  - In the //Pathways// panel select all the pathways (by default).
  - In the //Job information// panel, press the //File browser// button and select the desired output folder. In this case we will use //analysis//. Give a name to the job, for example "BRCA Differential signaling".

{{ :hipathia_work3.png?600 |}}

  - Press the //Launch job// button. A job will be created and listed in the jobs panel. You can access this panel by clicking on the //My jobs// button.
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