[BioC] Annotation Questions

John Zhang jzhang at jimmy.harvard.edu
Mon Dec 8 18:59:57 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?

You are right.

>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?

No, users are responsible for providing a file with the required mappings.  

>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)?

type ?function name (e. g. ?fileMuncher) will show the help page for the 

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


envokes a widget that allows users to explore the vignettes of installed 
packages without having to type the code.

>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?

Why do'nt you type your code in a text editor and then cut/paste your code to R.

>>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,
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

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