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--- worked_example_prediction [2021/01/07 20:45] – krian
+++ worked_example_prediction [2021/01/30 16:49] (current) – removed krian
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-====== Worked example Prediction  ======
-===== Test inputs =====
-**1.** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]].
-**2.** We will test the model with another Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix of the test data from the link:
-  * Test expression matrix: {{:brca_genes_vals_bn_test.txt|}}
-**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]].
-**4.** Click //Prediction// button.
-{{ :hipathia_bar_pred.png?600 |}}
-**5.** In the //Type// panel, select //Test existing predictor//. A window with all the existing models will appear. Select the model you want to use. We will use the model we have created in [[worked_example_prediction_-_train|Worked example Prediction - Train]]. The model information will appear on the right panel.
-{{ :hipathia_work5.png?600 |}}
-**6.** In the //Input data panel// select //Expression matrix//. Press the //File browser// of the //Expression matrix file//, and select the desired file, //brca_genes_vals_bn_test.txt//.
-{{ :hipathia_work6.png?600 |}}
-**7.** In the //Job 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 test model".
-{{ :hipathia_work7.png?600 |}}
-**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.
-===== 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).
-{{ ::testreport.png?nolink |}}
-==== Study Information ====
-Here you can find the information about the selected study.
-  * **Name**: the study name.
-  * **Description**: the description of the current study.
-  * **Tool**: the name of the used tool (in this case, is Hipathia).
-  * **Date**: study's launching date (MM/DD/AAAA, HH:MM:SS AM/PM format)
-==== Input Parameters ====
-Here you can find the parameters with which the current study was launched.
-{{ ::inputpredictreport.png?nolink |}}
-  * **Expression file**: The name of the expression file that has been used in the current study.
-  * **Species**: The species of this experiment; Human (Homo sapiens),Mouse (Mus musculus) or Rat (Rattus norvegicus).
-==== Circuit values ====
-You can download the matrix of circuit activity values by clicking on circuit values.
-This matrix file indicates for each "effector circuit" the level of activation calculated using Hipathia method for each sample.
-==== 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 results//.
-===== Prediction evaluation =====
-Confusion Matrix and Statistics
-      	     Reference
-Prediction LumA LumB
-  	LumA   95	5
-  	LumB	9   16
-           	Accuracy : 0.888
-% CI : (0.8192, 0.9374)
-	No Information Rate : 0.832
-	P-Value [Acc > NIR] : 0.0547
-              	Kappa : 0.6277
- Mcnemar's Test P-Value : 0.4227
-        	Sensitivity : 0.9135
-        	Specificity : 0.7619
-     	Pos Pred Value : 0.9500
-     	Neg Pred Value : 0.6400
-         	Prevalence : 0.8320
-     	Detection Rate : 0.7600
-   Detection Prevalence : 0.8000
-  	Balanced Accuracy : 0.8377