[BioC] Loading quantiles normalized root data in XPS

[Paul Geeleher]

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
>>
>>
>>
>



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com