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

cstrato cstrato at aon.at
Sun Aug 22 19:49:21 CEST 2010

Dear Daniel,

Sorry my mistake again!
After looking at my source code I realized that currently it is not 
possible to use a subset of trees only. Thus I have just uploaded to 
Bioconductor a new version "xps_1.8.3" which should solve the problem, 
and will be available within the next 1-2 days. You should now be able 
to use parameter "treename" to plot only a subset of trees.

Please let me know if the new version solves your problem.
Especially I am interested to know how many treenames you can pass to 
function root.profile() since there could be a limit on the number of 
characters you can pass to the root macro.

Since you mention that there are too many arrays to look reasonable on 
one plot, you could also change parameter "w" from the default "w=800" 
to e.g. "w=4000", especially if you save the plot by setting e.g. 

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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