[BioC] Error message from AnnBuilder
Hua Weng
hweng at biochem.okstate.edu
Wed Mar 29 00:52:32 CEST 2006
Hi, Ting-Yuan:
Thanks for the reply. After I updated AnnBuilder to version 1.9.16, I can
successfully build the following package for Cow. After I load this package,
I found I only have 7 environment variables as following:
> ls("package:AsithaBtPkg")
[1] "AsithaBtPkg" "AsithaBtPkgACCNUM" "AsithaBtPkgLOCUSID"
[4] "AsithaBtPkgMAPCOUNTS" "AsithaBtPkgORGANISM" "AsithaBtPkgQC"
[7] "AsithaBtPkgQCDATA"
I don't get any useful information back. See bellows:
> y <- as.list(AsithaBtPkgQCDATA)
> y
$name
[1] "AsithaBtPkg"
$built
[1] "Created: Tue Mar 28 16:16:17 2006 "
$probeNum
[1] 23
$numMissMatch
[1] "None"
$probeMissMatch
[1] "None"
$probeMapped
AsithaBtPkgACCNUM AsithaBtPkgLOCUSID
17 0
$otherMapped
AsithaBtPkgORGANISM
1
$sessionInfo
R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
[7] "datasets" "base"
other attached packages:
GO AnnBuilder RSQLite DBI annotate XML Biobase
"1.10.0" "1.9.16" "0.4-1" "0.1-10" "1.8.0" "0.99-6" "1.8.0"
My questions are:
1)If I provide more local annotation files, may I get more information back?
2)I didn't get any GO term back, does it mean these genes for cow don't have
any GO?
3)If I map these cow's Gene bank Accession ID to Mus musculus, can I get
some useful information back? Do I need to change cow's gene bank accession
IDs to Mouse's gene bank accession IDs?
Thank you very much for your response!
Hua
-----Original Message-----
From: Ting-Yuan Liu [mailto:tliu at fhcrc.org]
Sent: Tuesday, March 28, 2006 3:21 PM
To: Hua Weng
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: Error message from AnnBuilder
Hi Hua,
The "subscript out of bounds" bug had been fixed in the developmental
AnnBuilder, I believe. Please have a try.
HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________
On Tue, 28 Mar 2006, Hua Weng wrote:
>
> Dear List and Ting-Yuan:
> I finally decided to use AnnBuilder on Linux server. And I got sample data
> set, thgu95a, worked and I successfully installed the annotation package.
> But when I try to use one data set for cow (Bos taurus), I got the
following
> error message:
>
> Error in all(is.na(annotation[, "GO"])) : subscript out of bounds
>
> I don't know what does this error mean? Is it because my data set cannot
get
> any GO term?
>
> The code is as follow:
> > library("AnnBuilder")
> > myBase <- file.path("cluster6_Asitha_Bt.txt")
> > myDir <- "/home/hua/project/bioconductor/AnnBuilder/"
> > myBaseType="gbNRef"
> > mySrcUrls <-
> c(EG="file:////home/hua/project/bioconductor/AnnBuilder/gene_DATA",
> +
>
UG="file:////home/hua/project/bioconductor/AnnBuilder/UniGene/Bos_taurus/Bt.
> data.gz",
> +
>
GO="file:////home/hua/project/bioconductor/AnnBuilder/go_200603-termdb.rdf-x
> ml.gz")
> > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> myBaseType,
> + pkgName = "AsithaBtPkg", pkgPath = myDir, organism = "Bos taurus",
version
> = "1.1.0",
> + author = list(author = "Hua Weng", maintainer = "Hua Weng
> <hweng at biochem.okstate.edu>"), fromWeb = False)
>
> The following is data set look like:
> > myBase
> [1] "cluster6_Asitha_Bt.txt"
> > read.table(myBase, sep="\t", header=FALSE, as.is=TRUE)
> V1 V2
> 1 a2g09 NM_174062
> 2 g1o22 <NA>
> 3 a1d09 XM_879288
> 4 a1e10 NM_175825
> 5 g4n11 XM_873598
> 6 g1b02 <NA>
> 7 f7c16 <NA>
> 8 a1h04 XM_580317
> 9 f5l19 BC102351
> 10 g4p13 XM_879908
> 11 g4k22 NM_173968
> 12 f6d15 XM_874804
> 13 g4l22 XM_615696
> 14 g1h03 XM_873394
> 15 a1d10 NM_174658
> 16 f6c14 <NA>
> 17 g4k13 NM_001034575
> 18 f7k05 XM_868174
> 19 g4k23 <NA>
> 20 f6k09 NM_001007815
> 21 f6d16 NM_174792
> 22 g4f07 <NA>
> 23 f5k24 BT021073
>
> The first column is probe ID and the second column is Gene Bank accession
ID
> for Bos taurus. If I want to get the annotation for Mus musculus, can I
> still use the Gene bank accession ID for Bos Taurus?
>
> > sessionInfo()
> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
>
> attached base packages:
> [1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
> [7] "datasets" "base"
>
> other attached packages:
> GO AnnBuilder annotate XML Biobase
> "1.10.0" "1.8.0" "1.8.0" "0.99-6" "1.8.0"
>
> I highly appreciate any comments and suggestions.
>
> Thanks,
> Hua
>
>
> -----Original Message-----
> From: Ting-Yuan Liu [mailto:tliu at fhcrc.org]
> Sent: Friday, March 24, 2006 11:48 AM
> To: Hua Weng
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: AnnBuilder
>
>
> Hi Hua,
>
> Yes, you could run AnnBuilder in Windows system. That is not what I
> usually do, but I tried and succeed. However, my R in the windows
> machine is "built from source" (see section 3.1 of the manual "R
> Installation and Administration") and it might be a little different from
> your R (which is built from the binary installer, I guess.) Someone
> reported to me that it is unable to run AnnBuilder in the Windows system,
> but it did work in my machine. Therefore, you can try first to see if you
> can build annotation packages from the binary-installed R. If not, you
> should switch to the source-installed R.
>
> HTH,
> Ting-Yuan
> ______________________________________
> Ting-Yuan Liu
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> Seattle, WA, USA
> ______________________________________
>
> On Wed, 22 Mar 2006, Hua Weng wrote:
>
> > Hi, Bioconductor list and Ting-Yuan:
> >
> >
> >
> > I have problems in using AnnBuilder package.
> >
> >
> >
> > 1) May I use Windows based R environment to run ABPkgBuilder? I
> > haven't been successfully run this command. I saw there is a condition
> > before this command is "if(.Platform$OS != "windows" && interactive())",
> > Does this mean this command cannot run on windows platform?
> >
> > 2) I also tried to install AnnBuilder in R2.2.0 on Linux server.
But
> I
> > haven't been successfully installed it. The problem is before I could
> > install XML package, it gave me error message "**** You should use a
> > recent version of libxml2, i.e. 2.6.22 or higher ****". And when I
tried
> to
> > install 'libxml2', I got the following error:
> >
> > > install.packages("libxml2")
> >
> > Warning in download.packages(pkgs, destdir = tmpd, available =
available,
> :
> >
> > no package 'libxml2' at the repositories
> >
> > So I want to ask how I can successfully install 'libxml2' on Linux
server?
> >
> >
> >
> > > sessionInfo()
> >
> > R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
> >
> >
> >
> > attached base packages:
> >
> > [1] "methods" "stats" "graphics" "grDevices" "utils"
"datasets"
> >
> > [7] "base"
> >
> >
> >
> > 3) I found that UniGene source URL always point to 'Homo sapiens'
> data
> > even for the organism other than 'Homo sapiens'. Is that true?
> >
> >
> >
> > Thanks for your attention!
> >
> >
> >
> > Hua Weng
> >
> > Microarray Core Facility
> >
> > Oklahoma State University
> >
> > Department of Biochemistry and Molecular Biology
> >
> > 246 Noble Research Center
> >
> > Stillwater, OK 74078
> >
> >
> >
> >
>
>
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