[BioC] Generating GEO submission files from beadarray summary data

[Aliaksei Holik]

Hi Mark and Kemal,

The reason I needed the code in the first instance is because the 
GEOsubmission function produceGEOSampleInfoTemplate wouldn't work with a 
beadarray generated object. This is what I got in response from Tim Triche:

On 03/10/2012 15:56, Tim Triche, Jr. wrote:
 > yes, you need it to be a LumiBatch or other preprocessing-annotated
 > object in order for the information to be found
 >
 > ExpressionSetIllumina apparently doesn't contain that information.
 > try running traceback() after you get the error

Mind, this was more than a year ago and perhaps this functionality has 
been added.

All the best,

Aliaksei.

On 16/11/2013 06:50, Mark Dunning wrote:
> I just realised that there is already a 'GEOSubmission' package on
> Bioconductor. Did you already try this package? Perhaps this would be a
> more-logical place for the conversion script to exist?
>
> Mark
>
>
> On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat <kakat at mail.rockefeller.edu
> <mailto:kakat at mail.rockefeller.edu>> wrote:
>
>     Hi Aliaksei,
>
>     That would be great. Thanks.
>
>     I think it could be useful and if I recall correctly Mark or one of
>     the other others suggest to include it into the beadarray package.
>     Though, most of the users crave for RNA-seq tools I guess.
>
>     Best,
>     Kemal
>
>
>     On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador at bio.bsu.by
>     <mailto:salvador at bio.bsu.by>>
>       wrote:
>
>      > Hi Kemal,
>      >
>      > Mark's code needed some modifications, but I did manage to get it
>     to work. I'll send you both the original code and the one with
>     modifications.
>      >
>      > I wonder if it's worth making it into a package and what that
>     would involve.
>      >
>      > All the best,
>      >
>      > Aliaksei.
>      >
>      > On 15/11/13 3:48 AM, Kemal Akat wrote:
>      >> Hi all,
>      >>
>      >> It's an older post, but can anyone still provide the code
>     Aliaksei and Mark were talking about?
>      >>
>      >> Thank you.
>      >>
>      >> Kemal
>      >>
>      >> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048439.html
>      >>
>
>