worked_example_differential_example
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| ====== Worked example Differential signaling ====== | ====== Worked example Differential signaling ====== | ||
| + | {{:youtube.png?direct&30|https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be}}:https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be | ||
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| **1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]]. | **1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]]. | ||
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| **2-** 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: | **2-** 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: | ||
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| **3-** 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]]. | **3-** 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]]. | ||
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| **4-** Press the //Differential signaling// button. | **4-** Press the //Differential signaling// button. | ||
| - | {{ :hipathia_bar_diffsig.png?600 |}} | + | {{ :hipathia_bar_diffsig_5.png?600 |}} |
| - | **5-** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file. | + | **5-** In the //Input data panel//. Press the //File browser// of the //Expression matrix file//, and select the desired file. |
| {{ :hipathia_work1.png?600 |}} | {{ :hipathia_work1.png?600 |}} | ||
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| **7-** Select Human as species (by default). | **7-** Select Human as species (by default). | ||
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| **8-** In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//. | **8-** In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//. | ||
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| **9-** In the //Pathways// panel select all the pathways (by default). | **9-** In the //Pathways// panel select all the pathways (by default). | ||
| - | **10-** 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 |}} | + | **10-** In the //Study information// panel, press the //File browser// button and select the desired output folder. In this case we will use //analysis_BRCA//. Give a name to the study, for example "BRCA Differential signaling". |
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| + | {{ :hipathia_work3_5.png?600 |}} | ||
| - | **11-** 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. | + | **11-** Press the //Run analysis// button. A study will be created and listed in the studies panel. You can access this panel by clicking on the //My studies// button. |
worked_example_differential_example.1450787533.txt.gz · Last modified: 2020/04/03 20:18 (external edit)
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