hedenfalk {qvalue} | R Documentation

## P-values and test-statistics from the Hedenfalk et al. (2001) gene expression dataset

### Description

The data from the breast cancer gene expression study of Hedenfalk et al. (2001) were obtained and analyzed. A comparison was made between 3,226 genes of two mutation types, BRCA1 (7 arrays) and BRCA2 (8 arrays). The data included here are p-values, test-statistics, and permutation null test-statistics obtained from a two-sample t-test analysis on a set of 3170 genes, as described in Storey and Tibshirani (2003).

### Usage

    data(hedenfalk)

### Value

A list called `hendfalk` containing:

`p` | Vector of 3,170 p-values of tests comparing BRCA1 to BRCA2.
`stat` | Vector of 3,170 absolute two-sample t-statistics comparing BRCA1 to BRCA2.
`stat0` | A 3,170 by 100 matrix of absolute two-sample t-statistics from 100 independent permutations of the BRCA1 and BRCA2 labels; the row `stat0[i,].` contains the permutation statistics corresponding to observed statistic `stat[i]`.

### References

Hedenfalk I et al. (2001). Gene expression profiles in hereditary breast cancer. New England Journal of Medicine, 344: 539-548.

Storey JD and Tibshirani R. (2003). Statistical significance for genome-wide studies. Proceedings of the National Academy of Sciences, 100: 9440-9445.
http://www.pnas.org/content/100/16/9440.full

### See Also

`qvalue`, `empPvals`

### Examples

    # import data
    data(hedenfalk)
    stat <- hedenfalk$stat
    stat0 <- hedenfalk$stat0 #vector from null distribution

    p.pooled <- empPvals(stat=stat, stat0=stat0)
    p.testspecific <- empPvals(stat=stat, stat0=stat0, pool=FALSE)

    #compare pooled to test-specific p-values
    qqplot(p.pooled, p.testspecific); abline(0,1)

    # calculate q-values and view results
    qobj <- qvalue(p.pooled)
    summary(qobj)
    hist(qobj)
    plot(qobj)

[Package qvalue version 2.20.0 Index]