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

[cstrato]

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 <- 
root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))

# 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), 
c("TestA1","TestA2"))

# apply root.profile to subset
root.profile(subdata.test3)

Please let me know if this works for you.

Best regards
Christian


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
>>>
>