lung: DNA Microarray Data of Lung Tumors

In pvclust: Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling

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)

pvclust documentation built on Nov. 19, 2019, 5:07 p.m.