[BioC] xps: root.profile on a asubset of the data

cstrato cstrato at aon.at
Fri Aug 20 19:55:01 CEST 2010

Dear Daniel,

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
scheme.test3 <- 

# 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.

Best regards

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.
> Dan
> 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
>> 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 8/20/10 4:47 PM, Daniel Brewer wrote:
>>> Hello,
>>> 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
>>> them?
>>> Thanks
>>> Dan

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