[BioC] newbie problems with AnnBuilder

[Marc Carlson]

Hi Mark,

AnnBuilder is on its way out.  Please have a look at the SQLforge.pdf
vignette which can be found here:

http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html

If you have further questions after reading this, then please just ask,
and we should be able to help you out.


  Marc



Mark Kimpel wrote:
> I'm having problems getting AnnBuilder to work with the Affy Rat Gene ST
> array data supplied by Affy. Using the code chunk below, I am able to get
> AnnBuilder to create the annotation object, but it crashes, I believe, when
> it tries to save it. I should also mention that I had a previous crash when
> I had a madecdfenv package directory in place that used the same name. I got
> a "file lock" error, so I temporarily renamed the directory to see if this
> fixed the problem. As below, the error changed, but I still can't get the
> script to work.
>
> I suspect that there is a fundamental misunderstaning on my part related to
> how the annotation package should relate to the cdf package or some naming
> convention related to one or both.
>
> Mark
>
>   
>> require(AnnBuilder); require(makecdfenv)
>> myBase <- "RaGene-1_0-st-v1.na26.rn4.transcript.probe-entrez_gene.csv"
>> myBaseType <- "ll"
>> mySrcUrls <- getSrcUrl("all", "Rattus norvegicus")
>>
>> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
>>     
> +           myBaseType, pkgName =
> substring(cleancdfname("RaGene-1_0-st-v1"),
> +                         1, (nchar(cleancdfname("RaGene-1_0-st-v1")) - 3)),
> +           pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus
> norvegicus", version = "1.0",
> +           author = list(authors = "Mark W Kimpel", maintainer =
> +                           "mkimpel at iupui.edu"), fromWeb = TRUE)
> Read 1 item
> Read 1 item
> [1] "4450 2 2"
> Error in lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook) :
>   cannot open file
> '~/R_HOME/site-library-2.8.0/ragene10stv1/data/Rdata.rdb': No such file or
> directory
>
> Enter a frame number, or 0 to exit
>
> 1: ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> myBaseTy
> 2: makeLLDB(file.path(pkgPath, pkgName), compress = TRUE)
> 3: tools:::makeLazyLoadDB(dataEnv, dbbase, compress = compress)
> 4: lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,
> envhook)
> 5: function (e)
> 6: lazyLoadDBinsertValue(data, datafile, ascii, compress, envhook)
>
> Selection: 1
> Browse[1]> annotation[1:2,]
>      ENTREZID    PROBE      ACCNUM GO
> [1,] "100008565" "10766774" NA     NA
> [2,] "100034253" "10937540" NA     "GO:0005525 at IEA;GO:0005622 at IEA"
>      PMID                SYMBOL
> [1,] "16804107;17292978" "Slc39a4l"
> [2,] "8889548"           "Gnl3l"
>      GENENAME                                                     CHR
> [1,] "solute carrier family 39 (zinc transporter), member 4-like" NA
> [2,] "guanine nucleotide binding protein-like 3 (nucleolar)-like" "X"
>      MAP        REFSEQ                      UNIGENE     CHRLOC        PATH
> [1,] NA         "NM_001101021;NP_001094491" "Rn.10120"  "NA"          NA
> [2,] "Xq14-q21" "NM_001081958;NP_001075427" "Rn.164274" "-40301218 at X" NA
>      ENZYME PFAM                  PROSITE
> [1,] NA     "NA at IPI00817057"      "NA at IPI00817057"
> [2,] NA     "PF01926 at IPI00362844" "NA at IPI00362844"
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
>
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
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