dyebias.rgplot {dyebias} | R Documentation |
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
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, ...)
data |
The |
slide |
The index of the slide to plot; must be > 1, and < |
iGSDBs |
A data frame with intrinsic gene-specific dye biases,
the same as that used in |
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 |
output |
Specifies the output. If |
xlim,ylim, xticks, yticks,pch,cex,cex.lab |
Graphical parameters; see |
... |
Other arguments (such as |
None.
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.
Philip Lijnzaad p.lijnzaad@umcutrecht.nl
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.
dyebias.estimate.iGSDBs
,
dyebias.apply.correction
,
dyebias.rgplot
,
dyebias.maplot
,
dyebias.boxplot
,
dyebias.trendplot
## 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)