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@mail02.rd.taisyo.co.jp [mailto:Tore@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]
--------------------------------------------------------
This email is confidential and intended solely for the use
o...{{dropped}}
