Hi Fabio,

The current nuID annotation packages (named as lumixxxx, for example
lumiHumanV2) are organized in the same way as the Affymetrix annotation
packages. So if you want to find out how to map between nuID to Gene Name or
Gene Symbol, please take a look at ³annotate² package.
Actually, I gave an example in the lumi vignette of retrieve gene symbol
using ³getSYMBOL² function. Please check the vignette.
There is a general function ³lookUp² for retrieving annotation information.
For example, if you want to know the gene name, you can using the following
code:

nuIDs = c('usXvpKIKUjos7osMqA', 'ruJVS.6KCigOoFBRSE')
lookUp(nuIDs, 'lumiHumanV2', what='GENENAME')

Here nuIDs represents a vector of nuIDs, 'lumiHumanV2' is the annotation
library name, you can replace ŒGENENAME¹ with other categories you want to
convert from IDs. Please refer to the Œannotate¹ package for more details.


Happy holidays,



Pan



On 12/22/07 6:32 PM, "fabio manzo" <fabiomanzo25@gmail.com> wrote:

> Dear Dr. Pan Du,
> I know that i'm really bouring but i need to ask you another question , that
> i'm not able to solve. Can you help me to associate directly the nuID to gene
> name or if you can explain me how i can annotate the targetID or the probeID
> directly with the gene name. Thanks a lot and sorry again for the disturb.
> Best 
> fabio
> 
> 2007/12/21, Pan Du <dupan@northwestern.edu>:
>> Hi Fabio,
>> 
>> As shown in the use case in the vignette, you can directly use write.exprs
>> function. For example, suppose lumi.N is the normalized LumiBatch object,
>>  ## Output the data as Tab separated text file
>>> > write.exprs(lumi.N, file='processedExampleData.txt')
>> 
>> Tell me if you have any questions.
>> 
>> Pan
>> 
>> 
>> On 12/21/07 5:00 AM, "bioconductor-request@stat.math.ethz.ch
>> <mailto:bioconductor-request@stat.math.ethz.ch> "
>> <bioconductor-request@stat.math.ethz.ch> wrote:
>> 
>>> > Date: Fri, 21 Dec 2007 11:56:23 +0100
>>> > From: "fabio manzo" < fabiomanzo25@gmail.com
>>> <mailto:fabiomanzo25@gmail.com> >
>>> > Subject: [BioC] asking help for lumi package
>>> > To: bioconductor@stat.math.ethz.ch
>>> > Message-ID:
>>> > < 29f8b9360712210256y3d9ade23yf3bd1a4099dc8f28@mail.gmail.com
>>> <mailto:29f8b9360712210256y3d9ade23yf3bd1a4099dc8f28@mail.gmail.com> >
>>> > Content-Type: text/plain
>>> >
>>> > Dear everybody,
>>> > I'm Fabio Manzo, an italian phD student. I'm very new of the microarray
>>> > analysis data, and i got an Illumina dataset.  Using the lumi package  i
>>> > arrived  untill the  quantile normilization,but  i'mnot able to export the
>>> > dataset in .txt file. Can anibody help me?
>>> > Best, 
>>> > fabio
>>> >
>>> > [[alternative HTML version deleted]]
>> 
>> 
>> 



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