yeastCC {yeastCC}R Documentation

Data from the Spellman et al. (1998) yeast cell cycle microarray experiment

Description

This data package contains an exprSet instance for the yeast cell cycle microarray experiment. The dataset contains gene expression measures (log-ratios, with Cy3-labeled common reference) for 6,178 yeast genes in 77 conditions.

Usage

data(yeastCC)

Details

There are four main timecourses: alpha (alpha factor arrest), cdc15, cdc28, and elu (elutriation), corresponding to different synchronization methods. For details on experimental procedures and analysis, refer to Spellman et al. (1998) (in ../doc) and the Yeast Cell Cycle Analysis Project website (http://genome-www.stanford.edu/cellcycle/). The exprSet instance yeastCC was derived from the file "combined.txt" on the website. The ORF names for the 800 cell cycle regulated genes are stored in orf800.

Source

The raw data (images, TIFF) and processed data "combine.txt" used to create the exprSet instance yeastCC are available from the Yeast Cell Cycle Analysis Project website (http://genome-www.stanford.edu/cellcycle/). Gene annotation information is available from the Saccharomyces Genome Database (SGD, http://genome-www.stanford.edu/Saccharomyces/gene_list.shtml). The script "createYeastCC.R" for generating the yeastCC package is available in ../doc.

References

Spellman et al. (1998). Comprehensive Identification of Cell Cycle-regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Molecular Biology of the Cell, 9: 3273-3297 (../doc).

Examples

data(yeastCC)
yeastCC
varLabels(yeastCC)
pData(yeastCC)
description(yeastCC)
abstract(yeastCC)
geneNames(yeastCC)[1:10]
x <- exprs(yeastCC)
dim(x)

[Package yeastCC version 1.0.0 Index]