[BioC] xps: RMA background plot using ROOT graphics
cstrato
cstrato at aon.at
Tue Aug 3 21:43:29 CEST 2010
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
_._._._._._._._._._._._._._._._._._
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
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