hedenfalk: P-values and test-statistics from the Hedenfalk et al. (2001)...

Description Usage Value References See Also Examples

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

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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

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# 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)


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