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@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@IEA;GO:0005622@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@X" NA
     ENZYME PFAM                  PROSITE
[1,] NA     "NA@IPI00817057"      "NA@IPI00817057"
[2,] NA     "PF01926@IPI00362844" "NA@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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