R/hedenfalk.R

In qvalue: Q-value estimation for false discovery rate control

#' @name hedenfalk
#' @aliases hedenfalk
#' @title P-values and test-statistics from the Hedenfalk et al. (2001) gene
#'   expression dataset
#'
#' @usage data(hedenfalk)
#'
#' @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).
#'
#' @return A list called \code{hendfalk} containing:
#' \item{p}{Vector of 3,170
#' p-values of tests comparing BRCA1 to BRCA2.}
#' \item{stat}{Vector of 3,170
#' absolute two-sample t-statistics comparing BRCA1 to BRCA2.}
#' \item{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 \code{stat0[i,].}
#' contains the permutation statistics corresponding to observed statistic
#' \code{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. \cr
#' \url{http://www.pnas.org/content/100/16/9440.full}
#'
#' @seealso \code{\link{qvalue}}, \code{\link{empPvals}}
#' @examples
#' # import data
#' data(hedenfalk)
#' stat <- hedenfalk$stat
#' stat0 <- hedenfalk$stat0 #vector from null distribution
#'
#" # calculate p-values
#' 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)
#'
#' @keywords dataset, hedenfalk
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