[BioC] Exonmap mapping problems

[Michal Okoniewski]

Hi Tore, 

I cannot reproduce your results with my exonmap - in all the 
cases (except the first one of course) I get the same list of 12 exons. 
Your problem looks as if the result set is randomly truncated 
without producing any error. We have seen problems with translation 
function when the Ensembl database was corrupted, but it did not 
look exactly like that.. 
Could you please let me know if your results are reproducible in time
and 
between R sessions?

Cheers, 
Michal 

-----Original Message-----
From: Tore at mail02.rd.taisyo.co.jp [mailto:Tore at mail02.rd.taisyo.co.jp]
On Behalf Of Tore Eriksson
Sent: 27 August 2007 01:32
To: bioconductor at stat.math.ethz.ch
Subject: Exonmap mapping problems

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;L
C_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]
 
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