[BioC] help on AnnBuilder

Nianhua Li nialicn at yahoo.com
Tue May 29 16:18:20 CEST 2007

Hi, Pan,

Is "myBase" a file name or a character vector of GenBank accessions? It should 
be a file name. The file should be a text file with two columns delimited by 
tab. The file column should be ID (e.g. probeset ID), and the second should be 
genbank accessions in your case. Please also make sure "myBase" is edited in 
the same platform (linux/windows, etc) as the one you run AnnBuilder so that 
the return symbol (\n) is consistent.

You may also want to try 'baseMapType="gbNRef"', which covers both GenBank 
accessions (e.g. AK004566) and RefSeq accessions (e.g. NM_021600). This may 
give you a better annotation converage. But GenBank has include RefSeq 
accessions now-a-days, therefore "gb" may also work. Anyway, just FYI...



More information about the Bioconductor mailing list