[BioC] [XPS] integrating data processed outside of XPS into the tree

[cstrato]

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 at aon.at <mailto:cstrato at 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
>
>
>
>