[BioC] xps: RMA background plot using ROOT graphics
Daniel Brewer
daniel.brewer at icr.ac.uk
Tue Aug 3 17:55:47 CEST 2010
Hello,
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 =
unlist(treeNames(bgrd.rma))[1],canvas=unlist(treeNames(bgrd.rma))[1],save.as="png")
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?
Thanks
Dan
--
**************************************************************
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.
This e-mail message is confidential and for use by the a...{{dropped:2}}
More information about the Bioconductor
mailing list