[BioC] xps: RMA background plot using ROOT graphics

Daniel Brewer daniel.brewer at icr.ac.uk
Tue Aug 3 17:55:47 CEST 2010


I am using xps on exon array data and I have calculated the background
correction values using the RMA algorithm:

bgrd.rma <- express(rootData, "BgrdRMA", filedir = ".",tmpdir = "",
update = FALSE, bgcorrect.method = "rma", bgcorrect.select =
"antigenomic", bgcorrect.option = "pmonly:epanechnikov",
bgcorrect.params = c(16384),exonlevel="all")

I would now like to plot these calculated values using the ROOT graphics
rather than Rs plotting functions.

I have been doing:
root.image(bgrd.rma,treename =

but that appears to plot the wrong values (foreground corrected
values?).  I have tried adding leafname="fBg", but it says that that
leafnode does not exist.

Any ideas?


Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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