[BioC] AnnBuilder problem for mu11ksuba

[Ting-Yuan Liu]

Hi Dick,

A quick question:  what is the "myBaseType" value for the argument 
baseMapType?  It should be "ug" because your basefile is the mapping 
between probe ids and unigene ids.  

>From the information you provided, it is difficult for me to figure out 
where the problem is.  We are going to release mu11ksuba and mu11ksubb for 
the BioC 1.8, and I have built these two packages successfully.  We are 
testing them now and will put them on the repository for users to test 
soon.  In case you are still interested in building your own mu11ksuba,  
here are the code I used to build it:

    
ABPkgBuilder(baseName="mu11ksuba.GeneBankID",
                 baseMapType="gbNRef",
                 pkgName="mu11ksuba",
                 pkgPath=".",
                 organism="Mus musculus",
                 otherSrc=c(
               		EG="mu11ksuba.EntrezGeneID",
			UG="mu11ksuba.UniGeneID"
                   ),
                 version="1.11.20",
                 author=list(
                   authors="Ting-Yuan Liu, ChenWei Lin, Seth Falcon, 
Jianhua Zhang, James W. MacDonald",
                   maintainer="Ting-Yuan Liu <tliu at fhcrc.org>"
                   )
                 )

where 

mu11ksuba.GeneBankID:
aa000148_s_at	AA000148
AA000151_at	AA000151
aa000380_s_at	AA000380
aa000467_s_at	AA000467
aa000469_at	AA000469
...

mu11ksuba.EntrezGeneID:
aa000148_s_at	66164
AA000151_at	67467
aa000380_s_at	230908
aa000467_s_at	66119
aa000469_at	11772
...

mu11ksuba.UniGeneID:
aa000148_s_at	Mm.334789
AA000151_at	Mm.260767
aa000380_s_at	Mm.22453
aa000467_s_at	Mm.188339
aa000469_at	Mm.253090
...

You can parse these mappings from the annotation file Affymetrix provides.  

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, Dick Beyer wrote:

> I am having difficulty building a metadata package for mu11ksuba and was 
> hoping someone would look at the error message and give me some suggestions as 
> to what I am doing wrong. I am trying to follow the example in ABPrimer.pdf.
> 
> sessionInfo() 
> R version 2.2.1, 2005-12-20, x86_64-unknown-linux-gnu
> 
> attached base packages: 
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils" 
> [7] "datasets"  "base"
> 
> other attached packages:
>   AnnBuilder    annotate         XML       limma    siggenes      qvalue
>      "1.8.0"     "1.8.0"    "0.99-6"    "2.4.11"     "1.4.0"     "1.4.0"
>        gcrma matchprobes     annaffy        KEGG          GO        affy
>      "2.2.1"     "1.2.1"     "1.2.0"     "1.8.1"     "1.8.2"     "1.8.1"
>      Biobase
>      "1.8.0"
> 
> 
> myBase <- read.table("/home/dbeyer/Microarray/affy resourcerer 
> files/affy_Mu11KA UG for AnnBuilder.txt",sep = "\t", header = FALSE, as.is = 
> TRUE)
> 
> > myBase[1:5,]
>             V1        V2 
> 1 AA000151_at Mm.260767 
> 2 AA004127_at   Mm.3819 
> 3 AA009039_at  Mm.35837 
> 4 AA014405_at  Mm.29677 
> 5 AA014745_at Mm.275414
> 
> mySrcUrls <- getOption("AnnBuilderSourceUrls")  
> > mySrcUrls 
> $EG 
> [1] "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA" 
> $GEO 
> [1] "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?" 
> $GO 
> [1] "http://www.godatabase.org/dev/database/archive/latest" 
> $GP 
> [1] "ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes" 
> $HG 
> [1] "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" 
> $KEGG 
> [1] "ftp://ftp.genome.ad.jp/pub/kegg/pathways" 
> $LL 
> [1] "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" 
> $UG 
> [1] "ftp://ftp.ncbi.nih.gov/repository/UniGene" 
> $YG 
> [1] "ftp://genome-ftp.stanford.edu/pub/yeast/data_download/" 
> $AT 
> [1] "ftp://ftp.arabidopsis.org/home/tair/" 
> $IPI 
> [1] "ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/" 
> $CMAP 
> [1] "ftp://ftp1.nci.nih.gov/pub/CMAP/"
> 
> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType,
>   pkgName = "mu11ksuba", pkgPath = ".", organism = "Mus musculus", version = 
> "1.0", author = list(author = "dbeyer", maintainer = 
> "dbeyer at u.washington.edu"),  fromWeb = TRUE)
> 
> Error in validObject(.Object) : invalid class "EG" object: invalid object for 
> slot "baseFile" in class "EG": got class "data.frame", should be or extend 
> class "character"
> 
> Thanks very much for any help or suggestions, 
> Dick 
> ******************************************************************************* 
> Richard P. Beyer, Ph.D. University of Washington 
> Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 
> Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
>     Seattle, WA 98105-6099 
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html 
> http://staff.washington.edu/~dbeyer
> 
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