[BioC] AnnBuilder package: problem with gbNRef

Craddock, Richard C. (CDC/NCID/VR) (CTR) cmi5 at cdc.gov
Wed Jul 26 19:18:04 CEST 2006

Good morning,

Thank you for your reply Nianhua.  The base file that I have created is
probeset ID to a mixture of GenBank Accession and Ref Seq, thus
presumably "gbNRef" is the appropriate base type.  I have tried updating
my annotations to the latest version supplied by the vendor, and still
haven't had any luck.

Here is the file structure that I have created for the local copies of
the files:

/home/cameron/microarray_data/annotate          contains the EG files
/home/cameron/microarray_data/annotate/UniGene/Homo_sapiens  contains
the UniGene files
/home/cameron/microarray_data/annotate/KEGG/pathways contains the
contents of the KEGG pathway.tar.gz file.

It would seem to me that if there were a problem with finding the
appropriate date files that I would receive an error message.  I have
verified that the readURL and loadFromUrl functions work with the URLs I
have supplied.       

Here is a sample from my basefile:

> a
                      V1        V2
119    mwghum40K:A#09699 NG_002679
120    mwghum40K:A#10779 NM_014191
121    mwghum40K:A#00108 NM_016258
122    mwghum40K:A#00228 NM_005462
123    mwghum40K:A#00481  BC000631
124    mwghum40K:A#00652 NM_001167
125    mwghum40K:A#09199 NM_033341
126    mwghum40K:A#09493 NM_003310
127 mwgaracontrol#011-r1      <NA>
128    mwghum40K:A#09703  BT019423
129    mwghum40K:A#00277  CR614804
130    mwghum40K:A#00396 NM_002307
131    mwghum40K:A#00487 NM_004488
132    mwghum40K:A#00591    U43148
133    mwghum40K:A#05083 NM_012282
134    mwghum40K:A#05232 NM_006933
135    mwghum40K:A#05372 NM_003156
136    mwghum40K:A#05445  BC016055
137    mwghum40K:A#10328 NM_014254
138    mwghum40K:A#10675 NM_003263
139    mwghum40K:A#10903 NM_003794
140    mwghum40K:A#10992 NM_002456

Thanks for your help,


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