affySpikeIn {DEDS}R Documentation

Gene expression dataset from Affymetrix Spike-in Experiments

Description

The spike-in experiment represents a portion of the data used by Affymetrix to develop their MAS 5.0 preprocessing algorithm. Here we utilize the RMA (Irizarry et. al) probe level summaries. The data features 14 human genes spiked-in at a series of 14 known concentrations (0, 2^{-2}, 2^{-1}, ..., 2^{10} pM) according to a Latin square design among 12612 null genes. The data matrix affySpikeIn represents the two array groups among the 14 array groups that contain 12 replicates. Further details are available at http://www.affymetrix.com/analysis/download_center2.affx.

Usage

data(affySpikeIn)

Value

affySpikeIn matrix of gene expression levels measurements, rows correspond to genes (12626 genes) and columns to 24 samples.
affySpikeIn.L numeric vector indicating the sample class, 12 (code 0) vs. 12 (code 1).
affySpikeIn.gnames character vecter containing the names of the 12626 genes.
spikedgene numeric vector given the location of the 14 spiked genes.

References

R. A. Irizarry, B. M. Bolstad, F. Collin, L. Cope, B. Hobbs and T. P. Speed (2003) Summeries of affymetrix genechip probe level data. Nucleic Acide Research, 31:e15.


[Package DEDS version 1.0.3 Index]