data.raw {dyebiasexamples} | R Documentation

## 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)

[Package dyebiasexamples version 1.0.3 Index]