[BioC] Loading quantiles normalized root data in XPS

[cstrato]

Dear Paul,

The functions root.data(), root.call() and root.expr() were created to 
allow you access to the corresponding root files just in case that you 
did not save your R session.

In the cases where you compute expression levels stepwise, or only part 
of them such as normalize.quantiles(), as seems to be the matter in your 
case, there is no corresponding root.xxx() function to access the root 
file directly. In these cases you need to save your R session to have 
continued access to the resulting root file.

Please note that saving the R session is the usual case to have access 
to the root files.

Best regards
Christian


On 2/2/12 1:12 PM, Paul Geeleher wrote:
> Hi Christian,
>
> Thanks for your quick reply. I check what kind of trees I have using
> "getTreeNames()" as you'd suggested, it seems they are of type "cqu"
> rather than "int", this is presumably because my analysis required no
> background correction step?
>
> So I then tried:
>> data_qn<- root.expr(scheme.huex10stv2, "exon_quantiles.root", "cqu")
>
> but that gives me a huge number of errors that look like this:
>
> Error in<TFile::cd>: Unknown directory PreprocesSet
> Error: Could not get directory<PreprocesSet>.
> Error in<TFile::cd>: Unknown directory PreprocesSet
> Error: Could not get directory<PreprocesSet>.
> Error in<TFile::cd>: Unknown directory PreprocesSet
> Error: Could not get directory<PreprocesSet>.
> Error: Could not get tree<ExportSet>.
> Error in root.expr(scheme.huex10stv2, "exon_quantiles.root",  :
>    error in function ‘ExportData’
>
>
> This file "exon_quantiles.root" definitely exists in the current
> working directory though... Thanks again for your help!
>
> Paul.
>
>
>
> On Wed, Feb 1, 2012 at 9:01 PM, cstrato<cstrato at aon.at>  wrote:
>> Dear Paul,
>>
>> Please have a look at the help ?root.expr.
>>
>> If I understand you correctly, you did only do quantile normalization?
>>
>> To see the tree names in your file you should do:
>>> getTreeNames("exon_quantiles.root")
>>
>> You will probably see trees with extension "int", see help ?validTreetype.
>>
>> To load these trees you need to do:
>>> data_qn<- root.expr(scheme.huex10stv2, "exon_quantiles.root", "int")
>>
>> Please let me know if this did solve your problem.
>>
>> 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 2/1/12 7:07 PM, Paul Geeleher wrote:
>>>
>>> Hi,
>>>
>>> I've used xps to quantiles normalize (at probe level) some Affy Exon
>>> Array data. I now have a "root" file called "exon_quantiles.root", but
>>> if I try to load it the same was I'd load my raw data (using the
>>> scheme file I created for Affy exon arrays) I get the error below? I
>>> can load my raw data just fine though. Any ideas? Do I perhaps need a
>>> different "root scheme" file for this normalized data? Unfortunately,
>>> I haven't been able to find an answer.
>>>
>>>> scheme.huex10stv2<- root.scheme("huex10stv2.root")
>>>> data_qn<- root.data(scheme.huex10stv2, "exon_quantiles.root")
>>>
>>> Error in if (chipname != treetitle) { : argument is of length zero
>>>
>>> Hope someone can help,
>>>
>>> Paul.
>>>
>>>
>>>
>>>> sessionInfo()
>>>
>>> R version 2.11.0 (2010-04-22)
>>> x86_64-redhat-linux-gnu
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>>
>>
>
>
>