[BioC] Loading quantiles normalized root data in XPS

[Paul Geeleher]

Hi Christian,

Thanks for your quick and informative reply.

I have re-run the analysis and saved the R objects as you suggest. The
next thing I'm trying to do is to obtain the expression levels of the
probes, but this doesn't seem to be working for me:

> a <- validData(data_hapMap)
Error in .local(object, ...) : slot "data" has no data

Based on the documentation I think validData() is the correct function.

I've also performed probeset level DABG and I'm trying to set
individual probes which belong to probesets with DABG < .05 to 0 in
the expression matrix.

But it seems I can't see the expression matrix using validData().
Perhaps there is another function. Any ideas?

Thank you again for your help with this, I'm very grateful!

Paul.

On 2/2/12, cstrato <cstrato at aon.at> wrote:
> 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
>>>>
>>>>
>>>>
>>>
>>
>>
>>
>


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