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
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() .
|
None.
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, submitted
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)