worked_example_prediction
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- | ====== Worked example Prediction | ||
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- | ===== Test inputs ===== | ||
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- | **1.** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]]. | ||
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- | **2.** We will test the model with another Breast Cancer dataset (Luminal A Vs Luminal B) from the repository The Cancer Genome Atlas. | ||
- | You can download the expression matrix of the test data from the link: | ||
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- | * Test expression matrix: {{: | ||
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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]]. | ||
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- | **4.** Click // | ||
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- | {{ : | ||
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- | **5.** In the //Type// panel, select //Test existing predictor// | ||
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- | {{ : | ||
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- | **6.** In the //Input data panel// select // | ||
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- | {{ : | ||
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- | **7.** In the //Job information// | ||
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- | {{ : | ||
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- | **8.** 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. | ||
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- | ===== Test report===== | ||
- | As we said before, this experiment consists in test the trained model [[worked_example_prediction_-_train|(in this example)]], using another split of data (Luminal A or Luminal B). | ||
- | {{ :: | ||
- | ==== Study Information ==== | ||
- | Here you can find the information about the selected study. | ||
- | * **Name**: the study name. | ||
- | * **Description**: | ||
- | * **Tool**: the name of the used tool (in this case, is Hipathia). | ||
- | * **Date**: study' | ||
- | ==== Input Parameters ==== | ||
- | Here you can find the parameters with which the current study was launched. | ||
- | {{ :: | ||
- | * **Expression file**: The name of the expression file that has been used in the current study. | ||
- | * **Species**: | ||
- | ==== Circuit values ==== | ||
- | You can download the matrix of circuit activity values by clicking on circuit values. | ||
- | This matrix file indicates for each " | ||
- | ==== Prediction model ==== | ||
- | This is the most important result of our predictor, which is a matrix with three columns : | ||
- | * Sample name: all the 125 samples in the used expression matrix file. | ||
- | * Prediction: the predicted group LumB (Luminal B) or LumA (Luminal A) | ||
- | * Probability LumB: this is the probability of being lumB, if it is 1 that means the predictor is 100% sure that the given result will be LumB. | ||
- | You can download the matrix of predicted experimental design by clicking on // | ||
- | ===== Prediction evaluation ===== | ||
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- | ==== Confusion Matrix and Statistics ==== | ||
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- | ^ Reference | ||
- | ^ ^ | ||
- | ^ Prediction | ||
- | ^ ::: ^ LumB | 9 | 16 | | ||
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- | ^ Accuracy | ||
- | ^ 95% CI ||| (0.8192, 0.9374) | ||
- | ^ No Information Rate ||| 0.832 | | ||
- | ^ P-Value [Acc > NIR] ||| 0.0547 | ||
- | ^ Kappa ||| 0.6277 | ||
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- | ==== Mcnemar' | ||
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- | ^ P-Value | ||
- | ^ Sensitivity | ||
- | ^ Specificity | ||
- | ^ Pos Pred Value ||| 0.9500 | ||
- | ^ Neg Pred Value ||| 0.6400 | ||
- | ^ Prevalence | ||
- | ^ Detection Rat ||| 0.7600 | ||
- | ^ Detection Prevalence | ||
- | ^ Balanced Accuracy | ||
- | ===== Related papers ===== | ||
- | * https:// | ||
- | * https:// | ||
- | * https:// | ||
- | * https:// | ||
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worked_example_prediction.1610546254.txt.gz · Last modified: 2021/01/13 13:57 by krian