Entering edit mode
Law, Annie
▴
70
@law-annie-550
Last seen 10.2 years ago
Hi,
I am new to BioConductor and would appreciate advice with the
following.
My goal is to take cloneID's from for example Human microarray 19K
human
ESTs
and find out the corresponding accession number and subsequently
Unigene
identifier.
I would like to keep a database of this information.
I would also like to know if a cloneID has changed and if so note this
is the database and also update any corresponding information.
I would like to know what the best way is to proceed with this.
I have looked at the vignettes and it seems that the AnnBuilder
package should be used instead of the annotate package?
I went to the I.M.A.G.E. consortium and found out that they have an
ftp
site where I can download a file including information for all clones
including
IMAGE cloneID and Genbank accession numbers among other fields.
My first goal in this project would be able to compare my list of
cloneIDs
to
the file available on the I.M.A.G.E. consortium ftp site.
However, I don't think that I can use the ABPkgBuilder since it
requires a
text file with two columns and the I.M.A.G.E. consortium site is not
one of
the
accepted sites for the ABPkgBuilder.
Any suggestions?
If somehow I do get the list of my cloneIDs and corresponding
accession
numbers
I think I will be able to use the ABPkgBuilder. Is this true?
Also where can I look for information on dumping results form
AnnBuilder
into a database?
Are there tracking tools within BioConductor, AnnBuilder?
For example, is there a tracking tool available to let you know if a
cloneID
has changed?
what is the best way to create a user friendly interface with
BioConductor?
Is there a GUI interface tool available in the BioConductor package?
If not I may think of creating my own web interface or dumping the
information from the data base on an Excel sheet.
thanks very much for your help,
Annie.