[BioC] AnnBuilder problem for mu11ksuba

Thu Mar 23 20:26:18 CET 2006

Hi Ting-Yuan,

I am happy you and the other authors are making mu11ksuba and mu11ksubb for 1.8 soon.  If you would send me these two, I would love to test them.

Meanwhile, I would like to get ABPkgBuilder working. myBaseType="ug".  Do you need to have values for the otherSrc argument?

Thanks very much for your help,
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
*******************************************************************************

On Thu, 23 Mar 2006, Ting-Yuan Liu wrote:

>
> 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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>>
>