[BioC] annotations for Codelink arrays

Weiwei Shi helprhelp at gmail.com
Thu Apr 5 23:06:44 CEST 2007


Hi, there:
I am analyzing an expression profile using CodeLink RU1 arrays and
assume I could use the package called r10kcod for annotation. I did
some manual work before by using biomaRt and now I would like to try
this package. I searched the archives and found the following old post
(on 2005), discussing on a couple of issues like one2multiple mapping.
Here I am wondering how these problems have been solved in this new(?)
package.

Thanks,

Weiwei


On 10/17/05, John Zhang <jzhang at jimmy.harvard.edu> wrote:
>
> >So in this case, if some probes map to differents Entrez Gene ID's (that
> >is the case of some of the MULTIPLE probes in this chips, at least with
> >the company mappings) then it will be taken only one of the Entrez Gene
> >ID's (the smallest). I will have to check the company's mappings for these
> >probes to Entrez Gene or maybe not use it at all and be confident on
> >AnnBuilder method (best way a think).
>
> One to many mappings is always a problem as far as annotation is concerned.
> AnnBuilder makes a choice (may not be the best one) for the users when there are
> multiple Entrez Gene mappings for a given probe id. I would like to invite
> comments on what would be the best way of handling this situation.
>
>
> >
> >But how can I use a mixture of genebank ids (for most of the probes) and
> >unigene ids (for some of them)? If I use "gb" as baseMapType I will not
> >get the mapping for the unigene ids. If I use "ug" then the same for the
> >genbank ids. Cannot use the unigene ids in otherSrc because this can only
> >use Entrez ids. I worked a little with this with no good result. This is
> >briefly what I do:
>
> Currently there is no parser for both GB and UniGene ids. I will look into
> writing one. The go around for now is probably to map by GB and UG separately
> and then merge the results
>
> >
> >gb.txt: File with mappings from probe ids to genbank ids.
> >Sometimes I used a file ll.txt with mappings from probe ids. to locuslink
> >ids (mappings from the company) in otherSrc
>
> It is always a good idea to include otherSrc. AnnBuilder has a voting machenism
> that takes the mapping with the most votes from differenct sources.
>
>
> >
> >> library(AnnBuilder)
> >> myBase <- file.path("gb.txt")
> >> myBaseType <- "gb"
> >> mySrcUrls <- getSrcUrl("all", organism="Rattus norvegicus")
> >> myDir <- tempdir()
> >> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, baseMapType=myBaseType,
> >> pkgPath=myDir, organism="Rattus norvegicus", ... other parameters ...)
> >
> >
> >Thank you again for your help. I think this package is great and the best
> >way to deal with the nightmare of annotations out there.
> >
> >D.
> >
> >
> >> >
> >> >Thanks.
> >> >
> >> >D.
> >> >
> >> >El 13/10/2005, a las 3:14, Robert Gentleman escribió:
> >> >
> >> >> Hi Tao,
> >> >>   If the right set of mappings is available to get started, AnnBuilder
> >> >> is pretty easy to use. We can help you with the first one or two, and
> >> >> are happy to distribute them. If there is more widespread interest
> >> >> (and
> >> >> they are stable) we can add them to the build process.
> >> >>
> >> >>   Robert
> >> >>
> >> >> Shi, Tao wrote:
> >> >>
> >> >>> Any plans to create annotation packages for Codelink arrays?
> >> >>>
> >> >>> ...Tao
> >> >>>
> >> >>> _______________________________________________
> >> >>> Bioconductor mailing list
> >> >>> Bioconductor at stat.math.ethz.ch
> >> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >>>
> >> >>>
> >> >>
> >> >> --
> >> >> Robert Gentleman, PhD
> >> >> Program in Computational Biology
> >> >> Division of Public Health Sciences
> >> >> Fred Hutchinson Cancer Research Center
> >> >> 1100 Fairview Ave. N, M2-B876
> >> >> PO Box 19024
> >> >> Seattle, Washington 98109-1024
> >> >> 206-667-7700
> >> >> rgentlem at fhcrc.org
> >> >>
> >> >> _______________________________________________
> >> >> Bioconductor mailing list
> >> >> Bioconductor at stat.math.ethz.ch
> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >>
> >> >
> >> >_______________________________________________
> >> >Bioconductor mailing list
> >> >Bioconductor at stat.math.ethz.ch
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> >>
> >> Jianhua Zhang
> >> Department of Medical Oncology
> >> Dana-Farber Cancer Institute
> >> 44 Binney Street
> >> Boston, MA 02115-6084
> >>
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/bioconductor
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III



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