estrogen: Gene/Drug response dataset

In adaptMT: Adaptive P-Value Thresholding for Multiple Hypothesis Testing with Side Information

Description

P-values and ordering of genes drawn from a microarray dataset, consisting of 22283 genes on breast cancer cells in response to estrogen, from NCBI Gene Expression Omnibus (GEO) through 'GEOquery' package, with index "GDS2324".

Usage

estrogen

Format

An object of class data.frame with 22283 rows and 3 columns.

Details

The original dataset "GDS2324" consists of gene expression measurements for n = 22283 genes, in response to estrogen treatments in breast cancer cells for five groups of patients, with different dosage levels and 5 trials in each. The task is to identify the genes responding to a low dosage. The p-value for gene i is obtained by a one-sided permutation test which evaluates evidence for a change in gene expression level between the control group (placebo) and the low-dose group. The p-values are then ordered according to permutation t-statistics comparing the control and low-dose data, pooled, against data from a higher dosage (with genes that appear to have a strong response at higher dosages placed earlier in the list).

Two orderings are considered: first, a stronger (more informative) ordering based on a comparison to the highest dosage; and second, a weaker (less informative) ordering based on a comparison to a medium dosage.

The variables are as follows:

• pvals. p-values

• ord_high. stronger ordering

• ord_mod. weaker ordering

The R code to produce the data can be found in '/extdata/estrogen_get_pvals.R'.

adaptMT documentation built on May 1, 2019, 10:15 p.m.