Pan Zheng <zhpan99 at="" yahoo.com=""> writes:
> Hi,
>
> I am trying to build an annotation object with AnnBuilder for a
> GEO object (GPL285). The base is a list of Genbank accessions, and
> I would like to map them to EntrezGene ID.
> >
> When I used:
> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls,
baseMapType=c("gb"),
> pkgPath=myDir, organism="Mus musculus",pkgName = "mouseGPL285",
> version = "1.1.0",author = list(authors = "myname", maintainer =
> "myname at myemail.com"), fromWeb = T)
What is the value of myBase? Have you read the man page for
ABPkgBuilder and specified baseName as it describes? It think that is
the problem here.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
Center
http://bioconductor.org
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...
best
nianhua
