Example data for the dyebias package

Description

The dyebias-package, described in Margaritis et al. (2009) can be used to get rid of dye bias in two-colour microarrays. The data.raw and data.norm objects are used in its examples.

The objects represent four hybridizations of identical mRNA, with increasing Cy3 and Cy5 labeling percentages (identical per slide) and differently spiked-in external controls to judge the process of dyebias correction.

Usage

       data(data.raw)
       data(data.norm)

Format

The data uses the marray-package by Dudoit and Yang (2002). data.raw is a marrayRaw object, data.norm is a marrayNorm object derived from it by print-tip LOESS normalization. Neither is dyebias-corrected yet.

Details

The column R.group of maInfo(maTargets(data.norm)) shows the details. Eg., 4%_2EC indicates that the labeling (of both channels) was at 4%, and the external controls were spiked in at a concentration twice that of the green channel. See Margaritis et~al. (2009) for details.

Note

The Tuteja data is also included in this package under the (inst)/doc directory, as this data is not proper rda, tab or csv data. For details, refer to the original publication and/or the dyebias vignette.

Author(s)

Philip Lijnzaad

Source

All accession numbers below refer to ArrayExpress (http://www.ebi.ac.uk/microarray).

This two-colour microarrray data was obtained from identical mRNA extracts (protocol P-UMCU-37), spiked with external controls, dUTP-labeled with Cy3 and Cy5 (protocol P-UMCU-38). This was hybridized (protocol P-UMCU-39) onto self-spotted slides containing 70-mer oligonucleotides (2 replicates per oligo, Operon "Array-Ready", and including 2838 control features; protocol P-UMCU-34). Scanning was done with an Agilent G2565AA scanner (protocol P-UMCU-40) and images were quantified with BioDiscovery's ImaGene 7.x (protocol P-UMCU-42)

References

Margaritis, T., Lijnzaad, P., van~Leenen, D., Bouwmeester, D., Kemmeren, P., van~Hooff, S.R and Holstege, F.C.P. (2009). Adaptable gene-specific dye bias correction for two-channel DNA microarrays. Molecular Systems Biology, submitted

Dudoit, S. and Yang, Y.H. (2002) Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In: Parmigiani, G., Garrett, E.S. , Irizarry, R.A., and Zeger, S.L. (eds.) The Analysis of Gene Expression Data: Methods and Software, New~York: Springer

Examples

  data(data.raw)
  data(data.norm)