[BioC] AnnBuilder questions...

Dipl.-Ing. Johannes Rainer johannes.rainer at tugraz.at
Thu Mar 17 16:23:53 CET 2005


i wanted to build an annotation package for the Affymetrix rat2302 
chip. because i have problems to access ftp servers through the 
http_proxy i am behind (it works perfectly with http, but not through 
the ftp protocol) i downloaded the LocusLink and UniGene database files 
and created my UG and LL objects with the option "fromWeb=FALSE". i 
supposed that it would work, but i got an error "could not open 
connection to ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.info". i 
supposed the function would not try to establish connections to the 
internet when i submit the attribute fromWeb=FALSE and define a local 
url beginning with file:// . maybe this is a bug, it may be better if 
one can submit also the url of a local info file to get the information 
about the built that was used... i wrote a wrapper function that 
overwrites the getUGBuilt() function to read a local info file, but it 
took me some time to understand why the call everytime failed

another question: locuslink has been substituted by the Gene 
database... are there plans that AnnBuilder will annotate using the new 

thanks, jo

More information about the Bioconductor mailing list