[BioC] Generating GEO submission files from beadarray summary data
salvador at bio.bsu.by
Sat Nov 16 12:59:56 CET 2013
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
All the best,
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?
> 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.
> On Nov 14, 2013, at 4:39 PM, Aliaksei Holik <salvador at bio.bsu.by
> <mailto:salvador at bio.bsu.by>>
> > 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
> > 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
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