dyebias.trendplot {dyebias} | R Documentation |
The aim of this routine is to show the monotonicity of the total dye bias in the (uncorrected) data set. This is to judge whether the total dye bias of one reporter in one hybridization indeed behaves as the product of an intrinsic gene specific dye bias (iGSDB) and a slide specific factor (the slide bias), which is at the heart of the GASSCO method.
Showing the total dye bias of all reporters is too overwhelming,
therefore the medians of the total dye bias after binning by intrinsic
gene specific dye bias (as given in dyebias$dyebias
) are
plotted.
data |
The marrayNorm to trendplot.
|
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. Default should suffice in almost all cases. |
application.subset |
The set of reporters that was eligible for dye bias correction; same
argument as for dyebias.apply.correction .
|
n.bins |
The number of bins into which to classify the reporters, based on their intrinsic gene-specific dye bias. The median of each bin is plotted. |
type |
What to print for each bin and hybridization. Valid values are:
|
order |
If order==NULL , the slides are sorted by
increasing slide bias prior to boxplotting. This is typically done
for data that is not yet dye bias corrected. This order is also
returned as a value. If order!=NULL , the slides are put into
this order before trendplotting. This is typically done for a dye
bias-corrected data set, using the order of the uncorrected set. |
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. |
ylim, lty, lwd, main, sub, cex, xlab, ylab |
As for matplot() |
... |
Other arguments are passed on to matplot() . |
The order obtained, for use in a later call to this same function.
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.monotonicity
dyebias.monotonicityplot
## show trend plots of uncorrected and corrected next to each other: ylim <- c(-0.6, 0.6) layout(matrix(1:2, nrow=1,ncol=2)) order <- dyebias.trendplot(data=data.norm, iGSDBs=iGSDBs.estimated, # from e.g. dyebias.estimate.iGSDBs order=NULL, # i.e., order by increasing slide bias output=NULL, main="before correction", ylim=ylim ) order <- dyebias.trendplot(data=correction$data.corrected, # from dyebias.apply.correction iGSDBs=iGSDBs.estimated, order=order, # order by the original slide bias output=NULL, main="after correction", ylim=ylim )