dyebias.trendplot {dyebias}R Documentation

Creates a trend-plot of all reporters, binned by dye bias, with all slides ordered by slide bias.

Description

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.

Arguments

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:
    median
    Plot the bin-median: the median of all genes in that bin and hybridization
    mean
    Plot the mean of all genes in that bin and hybridization
    gene
    Plot the single gene that has the lowest squared distance to the bin-median over all hybridizations
    median.gene
    Plot the single gene that has the median squared distance to the bin-medians over all hybridizations
    worst.gene
    Plot the single gene that correlates worst with the bin-median over all hybridizations
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().

Value

The order obtained, for use in a later call to this same function.

Author(s)

Philip Lijnzaad p.lijnzaad@umcutrecht.nl

References

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

See Also

dyebias.estimate.iGSDBs, dyebias.apply.correction, dyebias.rgplot, dyebias.maplot, dyebias.monotonicity dyebias.monotonicityplot

Examples


                                       

  ## 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
                       ) 


[Package dyebias version 1.2.1 Index]