dyebias.rgplot: Produce scatterplots of the hybridization, with strongest dye...

In dyebias: The GASSCO method for correcting for slide-dependent gene-specific dye bias

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 [e-mail]

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)

dyebias documentation built on Nov. 8, 2020, 5:53 p.m.