[BioC] Exonmap mapping problems

[Tore Eriksson]

Hello everybody!

I have encountered some strange behaviour when using the mapping
functions in the exonmap package. The results are inconsistent for
different length inputs, and for long lists there is no result at all.
Some examples and the sessionInfo follows below. Shown are results for
probest.to.exon, but probeset.to.gene gives similar results. Any tips
are most welcome.

Tore

> xmapDatabase("Human")
Switching to human database...
done.
> length(sigs)
[1] 1865
> probeset.to.exon(sigs, debug=6)
elt.size 7 
list.size 8125 
num.lists 0 
extrabit  1 
Processing  1 th piece
NULL
> sigs[1:14]
 [1] "2315924" "2316106" "2318791" "2319627" "2320571" "2320764" "2321153"
 [8] "2321396" "2322705" "2323289" "2326877" "2328133" "2330669" "2331628"
> probeset.to.exon(sigs[1:9], debug=6)
elt.size 7 
list.size 8125 
num.lists 0 
extrabit  1 
Processing  1 th piece
 [1] "ENSE00001478357" "ENSE00001478400" "ENSE00001370617" "ENSE00001478362"
 [5] "ENSE00000862165" "ENSE00001400447" "ENSE00001422373" "ENSE00001469531"
 [9] "ENSE00001469483" "ENSE00001424556" "ENSE00001469369" "ENSE00001374956"
> probeset.to.exon(sigs[1:10], debug=6)
elt.size 7 
list.size 8125 
num.lists 0 
extrabit  1 
Processing  1 th piece
NULL
> probeset.to.exon(sigs[2:10], debug=6)
elt.size 7 
list.size 8125 
num.lists 0 
extrabit  1 
Processing  1 th piece
 [1] "ENSE00001478357" "ENSE00001478400" "ENSE00001370617" "ENSE00001478362"
 [5] "ENSE00000862165" "ENSE00001400447" "ENSE00001422373" "ENSE00001469531"
 [9] "ENSE00001469483" "ENSE00001424556" "ENSE00001469369" "ENSE00001374956"
> probeset.to.exon(sigs[2:11], debug=6)
elt.size 7 
list.size 8125 
num.lists 0 
extrabit  1 
Processing  1 th piece
[1] "ENSE00001478357" "ENSE00001478400" "ENSE00001370617" "ENSE00001478362"
[5] "ENSE00000862165"
> sessionInfo()
R version 2.5.0 (2007-04-23) 
ia64-unknown-linux-gnu 

locale:
LC_CTYPE=ja_JP.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=C;LC_PAPER=C;LC_NAME=C;LC_ADD
RESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=C;LC_IDENTIFICATION=C

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

other attached packages:
     exonmap        plier       RMySQL          DBI RColorBrewer   simpleaffy 
    "1.0.06"      "1.6.0"      "0.6-0"      "0.2-3"      "0.2-3"    "2.10.31" 
  genefilter     survival         affy       affyio      Biobase 
    "1.14.1"       "2.32"     "1.14.2"      "1.4.0"     "1.14.1" 
> 

$ mysqladmin version
mysqladmin  Ver 8.41 Distrib 5.0.45, for unknown-linux-gnu on ia64

_______________________________________________________________
Tore Eriksson [tore.eriksson ad po.rd.taisho.co.jp]