[BioC] Error message from AnnBuilder

Hua Weng hweng at biochem.okstate.edu
Wed Mar 29 22:53:52 CEST 2006


Hi Ting-Yuan:

As you suggested, I tried to use "live link" and get files through the web.
First I set source URL like this:
mySrcUrls <- c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",
UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Bos_taurus/Bt.data.gz",
GP="ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes",
GO="http://www.godatabase.org/dev/database/archive/latest",
KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathways")
I got the following errors:
Error in srcUrls[["KEGGGENOME"]] : subscript out of bounds
In addition: Warning message:
Organism Bos taurus is not supported by GoldenPath (GP). in:
getUCSCUrl(organism)

I changed the source URL as following, and then it works.
mySrcUrls <- c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",
UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Bos_taurus/Bt.data.gz",
	GO="http://www.godatabase.org/dev/database/archive/latest")
But I still get seven environments and nothing useful back. I checked my
Gene bank accession IDs, and they can map to Gene ID and UniGene ID and
possible GO information. Is this because AnnBuilder cannot handle the
organism other than Human, mouse and rat? Have you tested to build
annotation package for other organism such as Cow, Rice..?

Thank you very much for your advice.
Hua

-----Original Message-----
From: Ting-Yuan Liu [mailto:tliu at fhcrc.org] 
Sent: Wednesday, March 29, 2006 12:07 PM
To: Hua Weng
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: Error message from AnnBuilder


Hi Hua,

On Tue, 28 Mar 2006, Hua Weng wrote:

> My questions are:
> 1)If I provide more local annotation files, may I get more information
back?

Using more annotation files (basefiles) could improves the mapping 
results, but not the number of environments.  It is always a good idea to 
provide as many basefiles as you could.  

I am not sure why you didn't get many environments.  Could you try not to 
use local files to build annotation packages?  I mean you should remove 
the baseMapType and fromWeb arguments so that ABPkgBuilder could download 
the data from the web.  

> 2)I didn't get any GO term back, does it mean these genes for cow don't
have
> any GO?

No.  If cow doesn't have any associated Go information, you will get an 
environment whose values are all NAs.  See (1) for details to get more 
environments.  

> 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? 

I am not sure if I understand what you mean here.  Are you interested in 
the homology between cow and mouse?  The package btahomology might be 
what you want.  You can find it at
http://www.bioconductor.org/packages/data/annotation/1.8/html/btahomology.ht
ml

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

> 
> 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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