[BioC] Error message from AnnBuilder

[Hua Weng]

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
> 
>  
> 
>