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],s ave.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}}

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