[BioC] AnnBuilder questions...

[John Zhang]

>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

The code was trying to get the build information. Each of the objects (e. g. LL, 
UG, ...) has to be provided with a value for built to completely turn off the 
connection). We will try to figure out a better way of handling this. Thanks.

>
>another question: locuslink has been substituted by the Gene 
>database... are there plans that AnnBuilder will annotate using the new 
>database?
>
>thanks, jo
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084