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--- worked_example_prediction [2021/01/13 13:57] – [Prediction evaluation] 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 (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:
-  * 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              ^^^^
-^              ^             ^    Lum A    ^    LumB    ^
-^    Prediction    ^    LumA    |    95    |    5    |
-^    :::    ^    LumB    |    9    |    16    |
-^              Accuracy              |||    0.888    |
-^              95% 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 Rat              |||    0.7600    |
-^              Detection Prevalence              |||    0.8000    |
-^              Balanced Accuracy              |||    0.8377    |
-===== Related papers =====
-  * https://pubmed.ncbi.nlm.nih.gov/24521998/
-  * https://www.nature.com/articles/nature11412
-  * https://www.sciencedirect.com/science/article/pii/S096097761930596X
-  * https://www.annalsofoncology.org/article/S0923-7534(19)37122-4/fulltext