[BioC] Error message from AnnBuilder

Tue Mar 28 23:20:34 CEST 2006

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
> > 
> >  
> > 
> > 
> 
>