[BioC] AnnBuilder package: problem with gbNRef

[Nianhua Li]

Hi, Richard,

First to clarify, the patch in AnnBuilder v1.11.5 is useful only when the
baseFile is probe-to-Refseq mapping. If that is the case for your baseFile, your
baseType should be "refseq". You use baseType "gbNRef" only when your baseFile
is probeset ID to GenBank accession mapping.

If your baseFile is probe-to-GenBank mapping, then AnnBuilder should be able to
generate the correct result. In fact, all the annotation packages provided by
bioc core team are generated by AnnBuilder and the baseType are all "gbNRef". I
guess the reason you didn't get the expected output is because you didn't set
the local mirror of source data correctly. There is an instruction at
AnnBuilder/inst/doc/mirroringDataResources.rst. 

If you still have problem, please include the following information in your next
post so that your problem can be reproduced:
(1) A small part of your baseFile, just like what Weijun did.
(2) The file structure of your local mirror
(file:///home/cameron/microarray_data/annotate).

thanks

nianhua