[BioC] AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", etc)

[John Zhang]

But what was your base map type (baseMapType = ?)?

>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; 
h=Message-ID:Received:Date:From:Subject:To:Cc:MIME-Version:Content-Type:Content-
Transfer-Encoding; 
b=P1N/Dp4dpo+k/SKYAvznRmJqPOMk6UE6o6Txl319OQtLbcvooC7ztxQGQBKAKNCzwNqruklPTCJ1q2
11Gfreycwn//EL4XRFBA+tI/xtE9kwGvq1L10gqj/KbrjFg4uR9n1OCvjuw9RP+6i08MH08zDXLE+6aX
0P1PP9NfWIFjs=  ;
>Date: Sun, 9 Jul 2006 18:46:26 -0700 (PDT)
>From: Luo Weijun <luo_weijun at yahoo.com>
>Subject: AnnBuilder doesn't work on gene information ("GENENAME", "SYMBOL", 
etc)
>To: bioconductor at stat.math.ethz.ch
>Cc: jzhang at jimmy.harvard.edu
>MIME-Version: 1.0
>Content-Transfer-Encoding: 8bit
>X-PMX-Version: 5.2.0.266434, Antispam-Engine: 2.4.0.264935, Antispam-Data: 
2006.7.9.183432
>X-PMX-Spam: Probability=7%, Report='__CP_URI_IN_BODY 0, __CT 0, __CTE 0, 
__CT_TEXT_PLAIN 0, __DOMAINKEYS_YAHOO 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, 
__MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0'
>
>Hello all,
>I tried to build annotation with AnnBuilder package.
>The base file I used has probe names and mapped Entrez
>Gene IDs (human genes). Things worked fine, except
>some failed connection to KEGG database. And I got the
>final annotation package, and it works, that is really
>cool. However, I didn't see the gene information data,
>like "GENENAME", "SYMBOL" etc, though. And this
>information is important for a complete annotation of
>my customized microarray platform.
>I looked at annotation packages for affy chips, all
>have gene information data. However, the whole human
>genome annotation package, humanLLMappings, doesn't
>have it. And since these are also built with
>AnnBuilder, I think something stop working properly in
>my case and in humanLLMappings' case. 
>I studied the source codes from AnnBuilder package,
>and narrowed the problem down to the corresponding
>part in getAnnData function, which is called in
>ABPkgBuilder function. Here is that code chunk I
>extraced:
>
>    parser(srcObjs[["eg"]]) <-
>getBaseParsers("eginfo")
>    geneinfo <- try(parseData(srcObjs[["eg"]],
>srcObjs[["eg"]]@info, 
>        ncol = 5, mergeKey = FALSE))
>    colnames(geneinfo) <- c("PROBE", "SYMBOL",
>"GENENAME", "CHR", 
>        "MAP")
>    options(show.error.messages = TRUE)
>    if (inherits(annotation, "try-error")) {
>        stop(paste("Parsing Entrez Gene gene_info.gz
>failed because of:\n\n", 
>            annotation))
>    }
>    if (nrow(geneinfo) > 0) 
>        annotation <- merge(annotation, geneinfo, by =
>"PROBE", 
>            all.x = TRUE)
>
>I am not sure what problem happens here, but there is
>no error message shown, and which means I did get
>something assigned to geneinfo, but geneinfo is not
>merge into annotation, very likely it has 0 rows. 
>I am not sure I am correct here, but please let me
>know if you have any idea, and you know how to solve
>this problem. Thank you so much in advance. 
>
>Here is the code I use to build my annotation
>¡­
>ABPkgBuilder(baseName = myBase, baseMapType =
>myBaseType,
>pkgName = "hs95av2Entrezg7", pkgPath = myDir,
>organism = "Homo sapiens", version = "1.1.0", author =
>list(authors = "Weijun",
>maintainer = "Weijun <luo_weijun at yahoo.com>"), fromWeb
>=T)
>print(date())
>
>And my sessionInfo
>Version 2.3.1 (2006-06-01) 
>powerpc-apple-darwin8.6.0 
>
>attached base packages:
>[1] "tools"     "methods"   "stats"     "graphics" 
>"grDevices" "utils"    
>[7] "datasets"  "base"     
>
>other attached packages:
>AnnBuilder    RSQLite        DBI   annotate        XML
>   Biobase 
>  "1.10.0"    "0.4-1"   "0.1-10"   "1.10.0"   "0.99-7"
>  "1.10.0" 
>
>
>Weijun
>
>
>__________________________________________________
>Do You Yahoo!?
>Tired of spam?  Yahoo! Mail has the best spam protection around 
>http://mail.yahoo.com 

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