[BioC] Looking for R package for Nimblegen expression data

[Xinxia Peng]

Great. I will do that.

Thanks,
Xinxia  

-----Original Message-----
From: Todd Richmond [mailto:todd at nimblegen.com] 
Sent: Thursday, February 01, 2007 1:28 PM
To: Xinxia Peng
Cc: Benilton Carvalho; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Looking for R package for Nimblegen expression data

Hi Xinxia,

With apologies to Benilton, XYS files are not yet part of the standard
deliverables from our service lab. However, you can request them from
Tech Services and they will provide them for any recent order.

Regards,
Todd

Xinxia Peng wrote:
> I was told by Nimblegen that the XYS file is not always available for 
> expression data. Any suggestions?
> 
> Thanks,
> Xinxia
> 
> 
> -----Original Message-----
> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
> Sent: Monday, January 29, 2007 10:00 AM
> To: Xinxia Peng
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Looking for R package for Nimblegen expression 
> data
> 
> Yes, my bad not mentioning that... it's in the devel branch and it 
> does requires R-2.5.0.
> b
> 
> On Jan 29, 2007, at 12:58 PM, Xinxia Peng wrote:
> 
>> Great. Is it the devel package? It seems that it needs R 2.5.0?
>>
>> Xinxia
>>
>> -----Original Message-----
>> From: Benilton Carvalho [mailto:bcarvalh at jhsph.edu]
>> Sent: Monday, January 29, 2007 9:49 AM
>> To: Xinxia Peng
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] Looking for R package for Nimblegen expression 
>> data
>>
>> The oligo package handles those, and you'll need to use the 
>> makePlatformDesign package to build the data pkg required for 
>> analysis.
>>
>> The following might be helpful:
>>
>> http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/
>> tutorial-slides.pdf
>>
>> and contact me if you need any help regarding this, given that the 
>> documentation is not ready.
>>
>> b
>>
>> On Jan 29, 2007, at 12:18 PM, Xinxia Peng wrote:
>>
>>> Hello,
>>>
>>> Could someone suggest a R package for handling Nimblegen expression 
>>> arrays?
>>>
>>> Thanks,
>>> Xinxia
> 
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> 


--
Todd Richmond, PhD
Manager of Research Informatics
NimbleGen Systems, Inc
Madison, WI 53719
1-608-218-7600