Question: Plotting together data from hgu133a and b
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gravatar for raffaele calogero
15.2 years ago by
Italy/Turin/University of Torino
raffaele calogero500 wrote:
Hi, I would like to get in a unique chromosome plot both the data present in hg133a and in hgu133b. Since the geneplotter library needs a data package to build che chromosome location instance ChrClass.a<-buildChromLocation("hgu95av2") there is any way to combine the hgu133a and hgu133b data package? Raf -- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705410 Lab. ++39 0116705408 Fax ++39 0119038639 Mobile ++39 3333827080 email: raffaele.calogero@unito.it www: www.bioinformatica.unito.it
hgu133a hgu133b geneplotter • 472 views
ADD COMMENTlink modified 15.2 years ago by rgentleman5.5k • written 15.2 years ago by raffaele calogero500
Answer: Plotting together data from hgu133a and b
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gravatar for rgentleman
15.2 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
Well, I do not think that there is anything automatic, but you should be able to do something like: 1) create one for each of your two chips 2) class?chromLocation gives: Slots: 'organism': Object of class "character". The organism that these genes correspond to. 'dataSource': Object of class "character". The source of the gene data. 'chromLocs': Object of class "list". A list which provides specific location information for every gene. 'probesToChrom': Object of class "genEnv". A hash table which will translate a probe identifier to chromosome it belongs to. 'chromInfo': A numerical vector representing each chromosome, where the names are the names of the chromosomes and the values are their lengths 'geneSymbols': An environment that maps a probe ID to the appropriate gene symbol So the important things are to merge the chromLocs, the probesToChrom and the geneSymbols (the other stuff had better be the same), and to then insert these back into the object. z <- buildChromLocation("hgu95av2") slotNames(z) > ml1 = z@chromLocs > names(ml1) [1] "1" "10" "10_random" "11" "12" "13" [7] "14" "15" "16" "17" "17_random" "18" [13] "19" "1_random" "2" "20" "21" "22" [19] "2_random" "3" "4" "5" "6" "6_random" [25] "7" "7_random" "8" "8_random" "9" "9_random" [31] "Un_random" "X" "Y" "X_random" "3_random" "15_random" These are not in any order, so you should just be able to make a new list that concatenates the values for each chromosome, then for probesToChrom stuff; > z@probesToChrom <environment: 0x3e8a628=""> w = as.list(z@probesToChrom) do the same for the other list, concatenate these and then do something like ne = new.env(hash=TRUE) z@probesToChrom=l2e(theconcatenatedlist, ne) and something not unlike that for the other part.... and you should be in business On Sat, Jul 24, 2004 at 03:58:06PM +0200, Raffaele Calogero wrote: > Hi, > I would like to get in a unique chromosome plot both the data present in > hg133a and in hgu133b. > Since the geneplotter library needs a data package to build che > chromosome location instance > > ChrClass.a<-buildChromLocation("hgu95av2") > > there is any way to combine the hgu133a and hgu133b data package? > > Raf > > -- > Prof. Raffaele A. Calogero > Bioinformatics and Genomics Unit > Dipartimento di Scienze Cliniche e Biologiche > c/o Az. Ospedaliera S. Luigi > Regione Gonzole 10, Orbassano > 10043 Torino > tel. ++39 0116705410 > Lab. ++39 0116705408 > Fax ++39 0119038639 > Mobile ++39 3333827080 > email: raffaele.calogero@unito.it > www: www.bioinformatica.unito.it > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+
ADD COMMENTlink written 15.2 years ago by rgentleman5.5k
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