This is very helpful. Thanks.

Thomas

2011/9/27 cstrato <cstrato@aon.at>

> Dear Thomas,
>
> Yes, it is possible, see the examples in the help files ?'intensity<-' and
> ?'expr<-'.
>
> ad 1, intensity<-
> You can create new raw data, e.g. a user of xps has once applied "vsn" to
> the raw data and then imported the result into DataTreeSet using
> 'intensity<-'. However, be careful since CEL-files will be created, see the
> help file.
>
> ad 2, expr<-
> In principle it is possible to import any result of preprocessing into an
> ExprTreeSet. For example you could use fRMA and then import the result using
> 'expr<-'.
>
> I hope that this is the information you are looking for, however it would
> be helpful if you could explain in more detail what you would like to do.
>
> Best regards
> Christian
>
>
>
> On 9/27/11 10:04 PM, thomas sierocinski wrote:
>
>> Dear Chrisitan,
>>
>> Thanks for your answer.
>>
>> Is there any way to assign a data matrix (created outside XPS) to a ROOT
>> tree?
>>
>> Cheers,
>>
>> Thomas
>>
>> 2011/9/24 cstrato <cstrato@aon.at <mailto:cstrato@aon.at>>
>>
>>
>>    Dear Thomas,
>>
>>    I was looking at the source code of fRMA, which currently supports
>>    only "hgu133a", "hgu133plus2", "mouse4302" arrays, and realized that
>>    it is not possible for  me to support fRMA, since it depends on
>>    pre-calculated public-domain data which you need, e.g.
>>    hgu133afrmavecs. For this reason I cannot support fRMA. However,
>>    keep in mind that fRMA still uses RMA as algorithm.
>>
>>    Best regards
>>    Christian
>>
>>
>>
>>    On 9/24/11 1:32 AM, thomas sierocinski wrote:
>>
>>        Dear All, Dear Christian,
>>
>>        I'm using XPS to process/analyse human Exon arrays.
>>        I would like to use fRMA (frozen Robust MultiArray Analysis) to
>>        normalize/summarize the data.
>>        I'd like to know if is there a way to summarize/normalize data
>> using
>>        fRMA in XPS.
>>        More generally, is there a way to process the data by other
>>        methods (non
>>        supported by XPS) and then use it in the XPS framework?
>>
>>        Cheers,
>>
>>        Thomas
>>
>>
>>
>>
>>


-- 
-----------------------------------------------------------
Thomas Sierocinski, PhD
Genomic Analyst
GenomeDx Biosciences Inc. | 201-1595 W. 3rd Ave
Vancouver, BC V6J 1J8 | Canada
*Phone: 604-569-0072 | Fax: 866-505-5161*
email: *thomas@genomedx.com*
http://www.genomedx.com

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