[BioC] Error message from AnnBuilder
hweng at biochem.okstate.edu
Tue Mar 28 21:56:06 CEST 2006
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 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:
> myBase <- file.path("cluster6_Asitha_Bt.txt")
> myDir <- "/home/hua/project/bioconductor/AnnBuilder/"
> mySrcUrls <-
> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
+ pkgName = "AsithaBtPkg", pkgPath = myDir, organism = "Bos taurus", version
+ author = list(author = "Hua Weng", maintainer = "Hua Weng
<hweng at biochem.okstate.edu>"), fromWeb = False)
The following is data set look like:
> read.table(myBase, sep="\t", header=FALSE, as.is=TRUE)
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?
R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
attached base packages:
 "tools" "methods" "stats" "graphics" "grDevices" "utils"
 "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.
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
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.
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
> 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
> 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:
>  "methods" "stats" "graphics" "grDevices" "utils" "datasets"
>  "base"
> 3) I found that UniGene source URL always point to 'Homo sapiens'
> 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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