[BioC] xps: RMA background plot using ROOT graphics

[cstrato]

Dear Daniel,

Simply replace treeNames(bgrd.rma) with bgtreeNames(bgrd.rma) and use 
leafname="fBg", as you correctly suggested.

If you want to see all trees stored in the ROOT file you can use:
 > getTreeNames(rootFile(bgrd.rma))

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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On 8/3/10 5:55 PM, Daniel Brewer wrote:
> 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