[BioC] Annotation Questions

Law, Annie Annie.Law at nrc-cnrc.gc.ca
Mon Dec 8 18:11:39 MET 2003


Thanks for your response regarding mapping IMAGE clone IDs to unigene.  
I have some further questions
I am not using Affymetrix arrays.  This is why I don't think that
the "Annotation CSV" files will help me?

It seems that in the examples on the vignettes that the starting point is 
a list containing Affymetrix probe id's and then Genbank accession numbers.
My starting point is a list of clone id's.  I will use the examples from
the Bioconductor parsers and investigate creating my own parser.  
However, when it comes to the mapping of clone id to accession number 
is there something in Bioconductor that I can use?

My next question would be could I use the function fileMuncher?
Also, how do I find out more about functions while using Bioconductor?
Other than looking at the code how can I find out more about
ABPkgBuilder(which I will
be doing)?

Also, is there a way of 'running' a vignette so that you don't have to type
everything in?

A minor but important question.  In R if you mistype a line like you are in
the middle
of typing a long if statement.  What keys can you hit so that you can fix
the if statement
without retyping the whole if statement?

>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
>and find out the corresponding accession number and subsequently Unigene
>I would like to keep a database of this information.

You can download the "Annotation CSV" (or other format) for your chip from  
"http://www.affymetrix.com/analysis/download_center.affx". The file contains

mappings to GenBank accession numbers, Unigene ids, and other information.

I was following along the "How to use AnnBuilder" vignette and got to the
I was not sure at the end on how to use the data package I had built.
Where can I go to find out more information on how to use a data package and
data packages in general? 

In your vignettes on AnnBuilder I can see that you are loading up your
base file,
specifying which sites to download data,
then there are calls to parsers.
For the next step I would like to know the main functions responsible for
I would like to know if there are some functions I can use for mapping or
I can look at to model after.


Can you suggest a good resource for takig XML information
and dumping it into a database?

thanks very much,

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