dyebias.boxplot {dyebias} | R Documentation |
The aim of this routine is to show the magnitude of the dye bias across the data set, as well as the extent to which the GASSCO method could get rid of it. Typically, two boxplots would be shown, one before, one after dye bias correction. For esthetic reasons, the boxplots are usually ordered by the overal slide bias of the uncorrected data set. See also Margaritis et~al. (2009), Fig.~1 and 3.
data |
The marrayNorm object to boxplot.
|
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 .
|
order |
If order==FALSE , no ordering of slides prior to boxplotting
takes place. 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 an order!=NULL , the slides are put
this order before boxplotting. This is typically done for a dye
bias-corrected data set, using the order of the uncorrected set.
(See also Fig. 3 in the paper). |
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 |
As for boxplot() |
... |
Other arguments (such as main , etc.)
are passed on to boxplot() .
|
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.trendplot
ylim <- c(-1, 1) layout(matrix(1:2, nrow=1,ncol=2)) order <- dyebias.boxplot(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.boxplot(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 )