dyebias.rgplot {dyebias} | R Documentation

## Produce scatterplots of the hybridization, with strongest dye biases highlighted.

### Description

Plots the log_2(R) vs. log_2(G) (or alternatively M vs. A) signal of one slide, highlighting the reporters with the strongest red and green dye bias. Two lines indicate two-fold change. See also Margaritis et al. (2009), Fig. 1

### Usage

    dyebias.rgplot(data, slide, iGSDBs, dyebias.percentile=5,
                   application.subset=TRUE, output=NULL, xlim =
                   c(log2(50),log2(50000)), ylim = c(log2(50),log2(50000)),
                   xticks = c(100,1000,10000,10000), yticks =
                   c(100,1000,10000,10000), pch = 19, cex = 0.3, cex.lab =
                   1.4, ...)

    dyebias.maplot(data, slide, iGSDBs, dyebias.percentile=5,
                   application.subset=TRUE, output=NULL, xlim = c(6,16),
                   ylim = c(-2,2), pch = 19, cex = 0.3, cex.lab = 1.4, ...)

### Arguments

`data` | The `marrayNorm` object to plot one slide of.
`slide` | The index of the slide to plot; must be > 1, and < `maNsamples(data)`
`iGSDBs` | A data frame with intrinsic gene-specific dye biases, the same as that used in `dyebias.apply.correction`, probably returned by `dyebias.estimate.iGSDBs`; see there for documentation.
`dyebias.percentile` | The percentile of intrinsic gene specific dye biases (iGSDBs) for which to highlight the reporters.
`application.subset` | The set of reporters that was eligible for dye bias correction; same argument as for `dyebias.apply.correction`.
`output` | Specifies the output. If `NULL`, the existing output device is used; if `output` is one of `"X11", "windows", "quartz"`, a new X11 (Unix)/windows (Windows)/quartz (Mac) device is created. If `output` is a string ending in one of `".pdf", ".png", ".eps", ".ps"` is given, a file of that name and type is created and closed afterwards.
`xlim,ylim, xticks, yticks,pch,cex,cex.lab` | Graphical parameters; see `par()`
`...` | Other arguments (such as `main` etc.) are passed on to `plot()`.

### Value

None.

### Note

The highlighted spots are all spots with an iGSDB that lies in the top- or bottom- `dyebias.percentile` of iGSDBS. That is, not just the estimator genes are highlighted.

### Author(s)

Philip Lijnzaad p.lijnzaad@umcutrecht.nl

### 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, 5:266, 2009. doi: 10.1038/msb.2009.21.

### See Also

`dyebias.estimate.iGSDBs`, `dyebias.apply.correction`, `dyebias.rgplot`, `dyebias.maplot`, `dyebias.boxplot`, `dyebias.trendplot`

### Examples

      ## show both an RG-plot and an MA-plot of the uncorrected data and the
      ## corrected data next to each other.

      slide <- 3                               # or any other other, of course

      layout(matrix(1:4, nrow=2,ncol=2, byrow=TRUE))

      dyebias.rgplot(data=data.norm,
                     slide=slide,
                     iGSDBs=iGSDBs.estimated,   # from dyebias.estimate.iGSDBs
                     main=sprintf("RG-plot, uncorrected, slide %d", slide),
                     output=NULL)

      dyebias.rgplot(data=correction$data.corrected,
                     slide=slide,
                     iGSDBs=iGSDBs.estimated,
                     main=sprintf("RG-plot, corrected, slide %d", slide),
                     output=NULL)

      dyebias.maplot(data=data.norm,
                     slide=slide,
                     iGSDBs=iGSDBs.estimated,
                     main=sprintf("MA-plot, uncorrected, slide %d",slide),
                     output=NULL)

      dyebias.maplot(data=correction$data.corrected,
                     slide=slide,
                     iGSDBs=iGSDBs.estimated,
                     main=sprintf("MA-plot, corrected, slide %d",slide),
                     output=NULL)

[Package dyebias version 1.48.0 Index]