[BioC] Error message from AnnBuilder
Ting-Yuan Liu
tliu at fhcrc.org
Wed Mar 29 20:06:46 CEST 2006
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.html
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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