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.

Note that `spYCCES` is an `ExpressionSet` instance with the same data and slightly different phenodata annotation.

### 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.

### Examples

    data(yeastCC)
    yeastCC
    varLabels(yeastCC)
    pData(yeastCC)
    description(yeastCC)
    abstract(yeastCC)
    featureNames(yeastCC)[1:10]
    dim(exprs(yeastCC))

[Package yeastCC version 1.2.8 Index]