hello, I am using the package "globaltest". I would like to test for the cytoband position of the probes (or chromosomes). i am trying to figure out how to build up a "hgu133aMAP2PROBE" environment which would have similar structure to hgu133aPATH2PROBE, but so far i was not able to ifnd a way. So far i have looked into the vignette for package AnnBuilder, but i was not able to find what i am looking for. any suggestion? is there any easier way which allows me to carry out this analysis without creating a "hgu133aMAP2PROBE"? thanks a lot, Dario Greco -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm

maybe try buildChromMap() or buildChromLocation.2() functions from the reb/ideogram packages. buildChromMap may be better if it a small number of specific bands are being examined buildChromLocation.2 may be better if you would like to construct something similar to a global MAP2PROBE. Note that these functions return chromLocation objects similar to buildChromLocation from the annotate package. ## example affy.bands <- buildChromMap("hgu133plus2",c("1p1","1p2","1p3")) cL <- chromLocs(affy.bands) cL[["1p1"]] -kyle > From: Dario Greco <dario.greco at="" helsinki.fi=""> > Organization: University of Helsinki > Reply-To: dario.greco at helsinki.fi > Date: Mon, 12 Dec 2005 15:07:52 +0200 > To: Bioconductor at stat.math.ethz.ch > Subject: [BioC] hgu133aMAP2PROBE...? > > hello, > I am using the package "globaltest". > I would like to test for the cytoband position of the probes (or chromosomes). > > i am trying to figure out how to build up a "hgu133aMAP2PROBE" environment > which would have similar structure to hgu133aPATH2PROBE, but so far i was not > able to ifnd a way. > So far i have looked into the vignette for package AnnBuilder, but i was not > able to find what i am looking for. > > any suggestion? is there any easier way which allows me to carry out this > analysis without creating a "hgu133aMAP2PROBE"? > > thanks a lot, > Dario Greco > > -- > > Dario Greco > > Institute of Biotechnology - University of Helsinki > Building Cultivator II > P.O.Box 56 Viikinkaari 4 > FIN-00014 Finland > > Office: +358 9 191 58951 > Fax: +358 9 191 58952 > Mobile: +358 44 023 5780 > > Lab WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/ > > Personal WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > This email message, including any attachments, is for the so...{{dropped}}

Hi Dario, We use the function "saveMat" in AnnBuilder to transform a matrix to an environment. Have a look at that and you can write your own function to create hgu133aPATH2PROBE environment. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Mon, 12 Dec 2005, Dario Greco wrote: > hello, > I am using the package "globaltest". > I would like to test for the cytoband position of the probes (or chromosomes). > > i am trying to figure out how to build up a "hgu133aMAP2PROBE" environment > which would have similar structure to hgu133aPATH2PROBE, but so far i was not > able to ifnd a way. > So far i have looked into the vignette for package AnnBuilder, but i was not > able to find what i am looking for. > > any suggestion? is there any easier way which allows me to carry out this > analysis without creating a "hgu133aMAP2PROBE"? > > thanks a lot, > Dario Greco > > -- > > Dario Greco > > Institute of Biotechnology - University of Helsinki > Building Cultivator II > P.O.Box 56 Viikinkaari 4 > FIN-00014 Finland > > Office: +358 9 191 58951 > Fax: +358 9 191 58952 > Mobile: +358 44 023 5780 > > Lab WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/ > > Personal WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

>> i am trying to figure out how to build up a "hgu133aMAP2PROBE" environment >> which would have similar structure to hgu133aPATH2PROBE, but so far i was not >> able to ifnd a way. >> So far i have looked into the vignette for package AnnBuilder, but i was not >> able to find what i am looking for. >> >> any suggestion? is there any easier way which allows me to carry out this >> analysis without creating a "hgu133aMAP2PROBE"? The following code should get you the mappings between map and probe ids. You may then save the mappings using saveMat. >temp <- eapply(hgu133aMAP, paste, sep = "", collapse = ";") >temp <- cbind(names(temp), unlist(temp)) >temp <- AnnBuilder:::getReverseMapping(temp) >map2Probe <- cbind(names(temp), unlist(temp)) >> >> thanks a lot, >> Dario Greco >> >> -- >> >> Dario Greco >> >> Institute of Biotechnology - University of Helsinki >> Building Cultivator II >> P.O.Box 56 Viikinkaari 4 >> FIN-00014 Finland >> >> Office: +358 9 191 58951 >> Fax: +358 9 191 58952 >> Mobile: +358 44 023 5780 >> >> Lab WebPage: >> http://www.biocenter.helsinki.fi/bi/dna-microarray/ >> >> Personal WebPage: >> http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm >> >> _______________________________________________ >> 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 >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084