[BioC] trouble with yeastann function in AnnBuilder

[John Zhang]

Sorry, I forgot to update the man page. base should be a file name. If you would 
like to build a annotation package, yeastPkgBuilder is the correct function to 
use. Thanks.



>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>Mime-Version: 1.0 (Apple Message framework v619.2)
>To: bioconductor at stat.math.ethz.ch
>From: Jacob Michaelson <jjmichael at comcast.net>
>Date: Wed, 2 Feb 2005 19:06:52 -0700
>Received-SPF: none (hypatia: domain of bioconductor-bounces at stat.math.ethz.ch 
does not designate permitted sender hosts)
>Received-SPF: none (hypatia: domain of jjmichael at comcast.net does not designate 
permitted sender hosts)
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Content-Disposition: inline
>Content-Transfer-Encoding: 7bit
>Subject: [BioC] trouble with yeastann function in AnnBuilder
>X-BeenThere: bioconductor at stat.math.ethz.ch
>X-Mailman-Version: 2.1.5
>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch>
>List-Unsubscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=unsubscribe>
>List-Archive: <https://stat.ethz.ch/pipermail/bioconductor>
>List-Post: <mailto:bioconductor at stat.math.ethz.ch>
>List-Help: <mailto:bioconductor-request at stat.math.ethz.ch?subject=help>
>List-Subscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=subscribe>
>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on  
pascal.dfci.harvard.edu
>X-Spam-Level: 
>X-Spam-Status: No, score=0.1 required=3.0 tests=FORGED_RCVD_HELO  autolearn=ham 
version=3.0.1
>
>I think I finally found what I need to build a decent Yeast 2.0 
>annotation package, but unfortunately, I keep getting errors.
>
>The base file needed for yeastann is a two-column matrix containing 
>probe ids and SGD accession numbers.  I created such a file by 
>whittling down Affymetrix's Yeast 2.0 CSV annotation file into those 
>two columns.
>
> From the AnnBuilder documentation for yeastann:
>
>Arguments
>
>base
>base a matrix with two columns. The first column is probe ids and the 
>second one are the mappings to SGD ids used by all the Yeast Genome 
>data files. If base = "", the whole genome will be mapped based on a 
>data file that contains mappings between all the ORFs and SGD ids
>
>I then imported the above file into R using:
>
> > yeastsgd=read.csv("yeastsgd.csv")
>
>and then
>
> > yeastsgd=as.matrix(yeastsgd)
>
>...just to be safe (although I also tried without and still got errors).
>
>Then I pasted the default function from the yeastann documentation, 
>substituting my yeastsgd matrix into the base =" " position as follows:
>
>yeastAnn(base = yeastsgd, yGenoUrl =
>+                  
>"ftp://genome-ftp.stanford.edu/pub/yeast/data_download/",
>+                  yGenoNames =
>+                  c("literature_curation/gene_literature.tab",
>+                  "chromosomal_feature/SGD_features.tab",
>+                  "literature_curation/gene_association.sgd"), toKeep =
>+                  list(c(6, 1), c(9, 2, 5, 6, 8, 11, 3), c(2, 5, 7)),
>+                  colNames = list(c("sgdid", "pmid"), c("sgdid",
>+                  "genename", "chr", "chrloc", "chrori", "description",
>+                  "alias"), c("sgdid", "go")), seps = c("\t", "\t",
>+                  "\t"), by = "sgdid")
>
>which immediately produced the error message (FYI in the "base" 
>position I tried both with and without quotes, both of which produced 
>errors):
>
>Error in file(file, "r") : unable to open connection
>In addition: Warning messages:
>1: the condition has length > 1 and only the first element will be used 
>in: if (probe2ORF == "") {
>2: only first element of `description' argument used
>3: cannot open file `1769308_at'
>
>I'm not sure why it keeps misunderstanding a matrix when the 
>documentation specifically calls for a matrix (for some reason it 
>thinks 1769308_at is a file and not a probe).
>
>I verified that the imported data contains the data in the proper 
>placement, which it does, and the dimensions seem to be correct:
>
> > dim(yeastsgd)
>[1] 10928     2
>
>Also FYI here's the error message when the above yeastann function is 
>implemented and yeastsgd is imported using read.csv, but not as.matrix:
>
>Error in read.table(probe2ORF, sep = "\t", header = FALSE, strip.white 
>= TRUE) :
>	argument 'file' must be a character string or connection
>In addition: Warning message:
>the condition has length > 1 and only the first element will be used 
>in: if (probe2ORF == "") {
>
>I'd really appreciate any help or suggestions.
>
>Thanks!
>
>--Jake Michaelson
>
>	[[alternative text/enriched version deleted]]
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084