[BioC] Fwd: Re: AnnBuilder-1.5.31 question

[Ting-Yuan Liu]

Hi Ivan,

I also post this to bioconductor mailing list because the mailing list is 
archived regularly and other users can search the archive to get useful 
information.  

There are some approaches you can try to see what happened here:

1)  Make sure there is no extra space on your basefile.  (check 
probes 108179, 108184, 108185, 108195, ect)

2)
How did you create your basefile?  By Excel?  Sometimes the basefile 
created by Excel (or other program) will have some extra and invisible 
characters.  In order to overcome this situation, you can read your 
basefile into R by the function read.table (or other similar function) 
and then write the data out again (by write.table, etc).  

Again, there are a lot of useful information in the bioconductor mailing 
list, and we encourage people to discuss on the list.  Please feel free to 
post your question on the list so that other experts could help and other 
users could learn.

HTH,
Ting-Yuan

On Tue, 4 Oct 2005 ivan.borozan at utoronto.ca wrote:

> 
> 
> ----- Forwarded message from ivan.borozan at utoronto.ca -----
>     Date: Mon,  3 Oct 2005 11:31:19 -0400
>     From: ivan.borozan at utoronto.ca
> Reply-To: ivan.borozan at utoronto.ca
>  Subject: Re: AnnBuilder-1.5.31 question 
>       To: John Zhang <jzhang at jimmy.harvard.edu>
> 
> Hi John,
> 
> Sorry to bug you about this again. The dev version (1.6.31) of AnnBuilder works
> fine for me except for one thing, my probes ID's are not properly formated once
> i try to list them (from the annotation package - see below) they contain
> additional spaces that were not there initially could you please tell me if this
> can be fixed ?
> 
> 
> my base file looks like :(i.e probe ids and accnumbers - separated by tab files)
> 
> 5548382	BM549033
> 29305	R14519
> 28821	R14442
> 28397	R14205
> 28361	R13372
> 37974	R61410
> 5737347	BM564491
> 24701	R38905
> 24605	T80488
> 
> etc ...
> 
> 
> but my probeIDs in the annotation package have additional spaces like:
> 
> >probeID<-ls(env=HumanBuild27092005CHR)
> 
> > probeID[1:9]
> [1] "1018338" "1020408" "1047069" "1048420" "1075122" " 108179" " 108184"
> [8] " 108185" " 108195"
> 
> 
> > sessionInfo()
> 
> R version 2.1.0, 2005-04-18, i686-pc-linux-gnu 
> 
> AnnBuilder   annotate        XML    Biobase 
>   "1.6.31"    "1.6.5"   "0.93-4"   "1.5.12" 
> 
> best regards,
> ivan   
> 
> 
> Quoting John Zhang <jzhang at jimmy.harvard.edu>:
> 
> > Hi, Ivan,>
> > 
> > Have you tried the devel version of AnnBuilder. I think the url has been 
> > modified in reaponse to the change of the source file. If you really want to
> > 
> > play with the source co
> de, it is in the function getUGBuilt in
> > getSrcBuilt.R.
> >  
> > 
> > >X-Original-To: jzhang at jimmy.harvard.edu
> > >Delivered-To: jzhang at jimmy.harvard.edu
> > >Date: Wed, 14 Sep 2005 16:46:01 -0400
> > >From: ivan.borozan at utoronto.ca
> > >To: John Zhang <jzhang at jimmy.harvard.edu>
> > >Subject: AnnBuilder-1.5.31 question 
> > >MIME-Version: 1.0
> > >Content-Transfer-Encoding: 7BIT
> > >User-Agent: Internet Messaging Program (IMP) 3.1
> > >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on  
> > pascal.dfci.harvard.edu
> > >X-Spam-Level: 
> > >X-Spam-Status: No, score=-2.6 required=3.0 tests=BAYES_00,NO_REAL_NAME  
> > autolearn=no version=3.0.1
> > >
> > >Hi John,
> > >
> > >i've got an error from AnnBuilder could you please tell me how do i change
> > >readURL(infoUrl)
> > >
> > >from 
> > >
> > >Error in readURL(infoUrl) : Can't read from
> > >url:ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info
> > >
> > >into
> > >
> > >"ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.info" 
> > >
> > >?
> > >
> > >
> > >
> > >
> > >ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> > >myBaseType,pkgName = "HumanBuild-14092005", pkgPath = myDir,organism =
> > "Homo
> > >sapiens", version = "1.1.0",author = list(author = "ib", maintainer =
> > >"ivan.borozan at utoronto.ca"),fromWeb = TRUE)
> > >
> > >
> > >Error in readURL(infoUrl) : Can't read from
> > >url:ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info
> > >
> > >
> > >thanks,
> > >
> > >Ivan Borozan PhD,
> > >Postdoctoral Fellow,
> > >Microarray Group, 
> > >Banting and Best Department of Medical Research,
> > >University of Toronto.
> > >phone : 416 946 3435
> > >e-mail: ivan.borozan at utoronto.ca
> > >
> > >
> > >
> > 
> > Jianhua Zhang
> > Department of Medical Oncology
> > Dana-Farber Cancer Institute
> > 44 Binney Street
> > Boston, MA 02115-6084
> > 
> > 
> 
> 
> -- 
> 
> Ivan Borozan PhD,
> Postdoctoral Fellow,
> Microarray Group, 
> Banting and Best Department of Medical Research,
> University of Toronto.
> phone : 416 946 3435
> e-mail: ivan.borozan at utoronto.ca
> 
> 
> 
> 
> 
> ----- End forwarded message -----
> 
> 
> -- 
> 
> Ivan Borozan PhD,
> Postdoctoral Fellow,
> Microarray Group, 
> Banting and Best Department of Medical Research,
> University of Toronto.
> phone : 416 946 3435
> e-mail: ivan.borozan at utoronto.ca
> 
> 
> 
> 
>