GOLUB {cancerclass} | R Documentation

## GOLUB DATA

### Description

Gene expression data from the leukemia microarray study of Golub et al. [1]. Dataset GOLUB has a dimention of 7129 genes in 72 tumors samples. Dataset GOLUB1 has a dimention of 3571 genes in 72 tumors samples. This dataset is filtered and preprocessed as described in [2].

### Usage

      data(GOLUB)
      data(GOLUB1)

### Value

Data and annotations are organized in a ExtressenSet of the package Biobase.

`GOLUB` | ExpressionSet (7129 genes in 72 tumors)
`GOLUB1` | ExpressionSet (3571 genes in 72 tumors)

### References

[1] Golub TR et al (1999), Molecular Classification of cancer: class Discovery and Class Prediction by gene expression monitoring, Science 286:531-7.
[2] Dudoit S, Fridlyand J (2002), A prediction-based resampling method for estimating the number of clusters in a dataset, Genome Biol. 3(7):RESEARCH0036.

### Examples

    ### nvalidate
    data(GOLUB1)
    nval <- nvalidate(GOLUB1[1:200, ])
    # Use only the first 200 genes for speed-up of the calculations
    plot(nval, type="xy")
    plot(nval, type="genes")
    plot(nval, type="samples")

    ### validate
    data(GOLUB1)
    val <- validate(GOLUB1[1:200, ])
    # Use only the first 200 genes for speed-up of the calculations
    plot(val, type="xy")
    plot(val, type="genes")
    plot(val, type="samples")

    ### fit und predict
    data(GOLUB1)
    train <- GOLUB1[, 1:38]
    test <- GOLUB1[, 39:72]
    predictor <- fit(train, method="welch.test")
    prediction <- predict(predictor, test, positive="AML", ngenes=50, dist="cor")
    plot(prediction, type="histogram", score="zeta")
    plot(prediction, type="curves", score="zeta")
    plot(prediction, type="roc", score="zeta")
    summary(prediction)

    ### loo
    data(GOLUB1)
    cv <- loo(GOLUB1, positive="AML", ngenes=10, method="welch.test", dist="cor")
    plot(cv, type="histogram", score="zeta")
    plot(cv, type="samples", score="zeta")
    plot(cv, type="curves", score="zeta")
    plot(cv, type="roc", score="zeta")

[Package cancerclass version 1.28.0 Index]