[BioC] Plotting together data from hgu133a and b

[Robert Gentleman]

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 at 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 at probesToChrom
<environment: 0x3e8a628>

 w = as.list(z at probesToChrom)

do the same for the other list, concatenate these 
 and then do something like

  ne = new.env(hash=TRUE)
 z at 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 at unito.it
> www:   www.bioinformatica.unito.it
> 
> _______________________________________________
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-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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