geNetClassifier (version 1.12.0)

externalValidation.probMatrix: Probability matrix.

Description

Generates the probability matrix.

Usage

externalValidation.probMatrix(queryResult, realLabels, numDecimals=2)

Arguments

queryResult

Object returned by queryGeNetClassifier

realLabels

Factor. Actual/real class of the samples.

numDecimals

Integer. Number of decimals to return.

Value

The probability matrix.

Details

A probability matrix contains the probabilities of assigning each assigned sample to each class. They help identifying where errors are likelly to occur even though there were not actual errors in the external/cross validation.

See Also

Main package function and classifier training: geNetClassifier Query the classifier: queryGeNetClassifier Query summary: querySummary External validation stats: externalValidation.stats

Examples

##########################
## Classifier training
##########################

# Load an expressionSet:
library(leukemiasEset)
data(leukemiasEset)

# Select the train samples: 
trainSamples<- c(1:10, 13:22, 25:34, 37:46, 49:58) 
# summary(leukemiasEset$LeukemiaType[trainSamples])

# Train a classifier or load a trained one:
# leukemiasClassifier <- geNetClassifier(leukemiasEset[,trainSamples], 
#    sampleLabels="LeukemiaType", plotsName="leukemiasClassifier") 
data(leukemiasClassifier) # Sample trained classifier

##########################
## External Validation
##########################
# Select the samples to query the classifier 
#   - External validation: samples not used for training
testSamples <- c(1:60)[-trainSamples]         

# Make a query to the classifier:
queryResult <- queryGeNetClassifier(leukemiasClassifier, leukemiasEset[,testSamples])

# Obtain the probability matrix for the assigned samples:
externalValidation.probMatrix(queryResult, leukemiasEset[,testSamples]$LeukemiaType)