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--- worked_example_prediction [2021/01/22 18:39] – [Discussion] krian
+++ worked_example_prediction [2021/01/30 16:49] (current) – removed krian
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-====== Worked example - Prediction  ======
-In this page we provide a walkthrough and a brief discussion of the Prediction tool. This comprises the [[worked_example_prediction_-_train | training of a model]] and its [[worked_example_prediction | testing]] with a different split of data.
-===== Test inputs =====
-**1.** Log into HiPathia. For further information on this step visit [[logging_in|Logging in]].
-**2.** Selection of test data. We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas (TCGA) [[https://portal.gdc.cancer.gov/projects/TCGA-BRCA | Link to dataset]].
-More information on the original dataset is available here:
-* [[https://www.nature.com/articles/nature11412]]
-* [[https://pubmed.ncbi.nlm.nih.gov/23644459/]]
-We have selected a subset of Breast Cancer samples from the dataset annotated as luminal A or luminal B (the molecular annotations come from [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465532/ | this paper]]) that **were not used in the training** of the model that we want to test.
-You can download the expression matrix we use to test the model from this link:
-  * Test expression matrix: [[http://hipathia.babelomics.org/data/brca_sub_class_exp_test.txt|brca_sub_class_exp_test.txt]]
-**3.** Upload the test data to HiPathia in the data panel by clicking //My data//. For further information on this step visit [[upload_your_data|Upload your data]].
-**4.** Click the //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. The model information will appear on the right panel. You can follow the steps in [[worked_example_prediction_-_train|Worked example Prediction - Train]] to train your own model with your data. We will test the model we have trained in that guided example.
-{{ :hipathia_work5.png?600 |}}
-**6.** In the //Input data// panel select //Expression matrix//. Click the //File browser// in the //Expression matrix file// section and select the desired file: //brca_genes_vals_bn_test.txt//.
-{{ :hipathia_work6.png?600 |}}
-**7.** In the //Job information// panel, click 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.** Click 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=====
-This section provides a walkthrough of the report page generated when testing a [[worked_example_prediction_-_train | previously trained model]] with another split of data.
-{{ ::testreport.png?nolink |}}
-==== Study Information ====
-Here appears 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 appear 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 ====
-The matrix of circuit activity values can be downloaded by clicking //circuit values//.
-This matrix file indicates for each "effector circuit" the level of activation calculated using the 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    |