R: DNA Microarray Data of Lung Tumors

lung {pvclust} | R Documentation

## DNA Microarray Data of Lung Tumors

### Description

DNA Microarray data of 73 lung tissues including 67 lung tumors. There are 916 observations of genes for each lung tissue.

### Usage

    data(lung)

### Format

data frame of size (916, 73).

### Details

This dataset has been modified from original data. Each one observation of duplicate genes has been removed. See `source` section in this help for original data source.

### Source

http://genome-www.stanford.edu/lung_cancer/adeno/

### References

Garber, M. E. et al. (2001) "Diversity of gene expression in adenocarcinoma of the lung", Proceedings of the National Academy of Sciences, 98, 13784-13789.

### Examples

    ## Reading the data
    data(lung)

    ## Multiscale Bootstrap Resampling
    lung.pv <- pvclust(lung, nboot=100)

    ## CAUTION: nboot=100 may be too small for actual use.
    ##          We suggest nboot=1000 or larger.
    ##          plot/print functions will be useful for diagnostics.

    ## Plot the result
    plot(lung.pv, cex=0.8, cex.pv=0.7)

    ask.bak <- par()$ask
    par(ask=TRUE)

    pvrect(lung.pv, alpha=0.9)
    msplot(lung.pv, edges=c(51,62,68,71))

    par(ask=ask.bak)

    ## Print a cluster with high p-value
    lung.pp <- pvpick(lung.pv, alpha=0.9)
    lung.pp$clusters[[2]]

    ## Print its edge number
    lung.pp$edges[2]

    ## We recommend parallel computing for large dataset as this one
    ## Not run:
    library(snow)
    cl <- makeCluster(10, type="MPI")
    lung.pv <- parPvclust(cl, lung, nboot=1000)

    ## End(Not run)

[Package pvclust version 2.0-0 Index]