[BioC] automatic data package maker

[Robert Gentleman]

On Dec 10, 2004, at 1:36 PM, Tomas Radivoyevitch wrote:

> Doing this manually has been taking me 1 to 2 hours a pop.
>
> Related to your question, a few weeks ago I tried to post the two  
> questions below. Regarding the second of these and your question,  
> perhaps the solution is to simply get everyone into the habit of  
> making R data packages and sending them up to Bioconductor. It would  
> be nice if manuscripts started coming with R scripts as "additional  
> files" so that figures could be reproduced, and having the  
> corresponding datasets up at bioconductor as R packages would  
> certainly help.
>
> Q1:   Does anyone have an automatic approach to grabbing GEO soft  
> files and making esets out of them?

   I think not, but things like readGEOAnn could be used for such  
purposes. If they do not fit your requirements please let us know as we  
would happily take patches/improvements (on these and virtually any  
other functions).

>
> Q2:   Regarding R Data packages as an alternative to grabbing things  
> from GEO, can anyone explain why there are so few (if any) GEO  
> datasets also up at Bioconductor? I'm wondering if there's some sort  
> of legal hindrance going on, or if it's just the leg work that's  
> missing.
>

   Just time, if you have some please feel free, and let us know if  
there is anything we can do to help...

    Robert



>
> ----- Original Message ----- From: "Rafael A. Irizarry"  
> <ririzarr at jhsph.edu>
> To: <bioconductor at stat.math.ethz.ch>
> Sent: Friday, December 10, 2004 2:58 PM
> Subject: [BioC] automatic data package maker
>
>
>> hi!
>>
>> is there a utility to automatically create a data package?
>>
>> if not, im making one cause i have tons of rdas lying around that i  
>> want
>> to load using library instead of load.
>>
>> it will take as input the location of an rda, location to save the
>> package, package title, package author, and text describing the data
>> (for the Rd file) and create a package for that data set.
>>
>> any auxiliary untility that i should be using?
>>
>> -r
>>
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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>
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>
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| Robert Gentleman              phone: (206) 667-7700            |
| Head, Program in Computational Biology   fax:                          
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