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.
dyebias.boxplot(data, iGSDBs, dyebias.percentile=5, application.subset=TRUE, order, output=NULL, ylim=c(-4,4), ...)
data |
The |
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 |
order |
If |
output |
Specifies the output. If |
ylim |
As for |
... |
Other arguments (such as |
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, 5:266, 2009. doi: 10.1038/msb.2009.21.
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 )