[BioC] problem with function to interrogate x:Map (exonmap)

[Wolfgang Raffelsberger]

Dear list,

following the instructions in the help-pages (exonmap.pdf) I get to a 
list of 'significant' exons/genes (sigs) but when interrogating xMap 
(which we have installed locally with the most recent version of mySQL) 
the query-functions always return empty vectors.

After looking more carefully the SQL tables we realized that by 
furnishing "Probeset ID" from Affymetrix gives correct results.
However, the function "names" used with "names(fc(pc.exonmap))[.." 
returns different identifiers and the corresponding Affymetrix "Probeset 
ID" are/would not be known at this stage of the analysis !
We realized that the table "probset.sql" allows to retreive such 
Affymetrix "Probeset ID" (given the names in sigs were mapped with the 
rownames of the expression-set).  But I don't see one of the functions 
of the package exonmap allowing to do such a query, am I incorrect ?.
Using the command, "featureNames" (following the example form 
"exonmap.example.pdf") we get the same result as with 
"names(fc(pc.exonmap))[.." , still an output in format that doesn't seem 
to be the correct one to the correct one for entering the pre-built SQL 
queries.

Any suggestions ?

Thank's in advance,
Wolfgang Raffelsberger


 > data(exonmap)
 > pc.exonmap <- pc(x.rma, "group", c("a", "b"))
 > sigs <- names(fc(pc.exonmap))[abs(fc(pc.exonmap)) > 1 & 
tt(pc.exonmap) < 1e-04]
 > length(sigs)                 # ger 31 entries
 > sigs[1:3]                    # look at the 1st 3 of them ...
[1] "3102398" "3102391" "3102439"
 >
 > xmapDatabase("Human")        # Switching to human database
Switching to human database...
done.
 > sig.exons <- probeset.to.exon(sigs)
 > length(sig.exons)                 # get NULL
 > probeset.to.transcript(sigs)      # get NULL
 > select.probewise(sigs, filter = "exonic")  # get NULL
 >
 > sigs <- c("3743907","3743908")  # here I enter some "Probeset ID" 
from Affymetrix (!) for p53
 > probeset.to.transcript(sigs)     # get correct result (but in normal 
case I won't know these IDs !)
 > probeset.to.exon(sigs)            # again OK
 >
 > sessionInfo()
R version 2.5.1 (2007-06-27)
x86_64-unknown-linux-gnu

locale:
C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
     exonmap        plier       RMySQL          DBI RColorBrewer   
simpleaffy
    "1.0.07"      "1.6.0"      "0.6-0"      "0.2-3"      "1.0-1"    
"2.10.31"
  genefilter     survival         affy       affyio      Biobase
    "1.14.1"       "2.32"     "1.14.2"      "1.4.1"     "1.14.1"




 

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. . .

Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
IGBMC
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
wolfgang.raffelsberger at igbmc.u-strasbg.fr