[BioC] xps: root.profile on a asubset of the data
cstrato at aon.at
Fri Aug 20 19:55:01 CEST 2010
Sorry my mistake!
As the help file says you can use parameter "treename" only to draw
different leaves for one tree.
In your case you need to define a subset of your dataset, e.g.:
# get scheme
# import all CEL-files
celdir <- "/Volumes/CoreData/ROOT/rootdata/testAB/raw"
data.test3 <- import.data(scheme.test3, "tmp_test3", celdir=celdir)
# define subset of CEL-files
subdata.test3 <- root.data(scheme.test3, rootFile(data.test3),
# apply root.profile to subset
Please let me know if this works for you.
On 8/20/10 5:35 PM, Daniel Brewer wrote:
> Hi Christian,
> I tried that, but it kicked up an error and only plotted one boxplot.
> It was like "treename" could only take one parameter. Maybe I was doing
> something wrong. I will have another go.
> On 20/08/2010 4:06 PM, cstrato wrote:
>> Dear Daniel,
>> You can simply use parameter "treename" to plot only a subset of trees,
>> see "?root.profile".
>> Best regards
>> 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 8/20/10 4:47 PM, Daniel Brewer wrote:
>>> I am using xps to do some quality control on an Affymetrix exon array
>>> experiment I am looking at. I am trying to use the ROOT graphics to
>>> plot density boxplots of the raw intensities (using root.profile). The
>>> problem is that there is too many arrays to look reasonable on one plot.
>>> Is there a way to split up the dataset into smaller pieces and plot
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