[BioC] Experiment export in Gene Expression Omnibus (GEO) SOFT format

[Henrik Hornshøj Jensen]

Thank you for clearing this up. 
To me it seems obvious to do the SOFT export in R as well.
Perhaps you could send the perl/R scripts you have been using.

Henrik
 


-----Oprindelig meddelelse-----
Fra: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sendt: Wednesday, May 24, 2006 12:55 PM
Til: Henrik Hornshøj Jensen; Bioconductor
Emne: Re: [BioC] Experiment export in Gene Expression Omnibus (GEO) SOFT format




On 5/24/06 5:23 AM, "Henrik Hornshøj Jensen" <HenrikH.Jensen at agrsci.dk>
wrote:

> Hi,
>  
> Anyone know if there is an R script or package for exporting 
> microarray experiments in SOFT file format for submission to GEO?
> Could be from expression data set objects, MA objects or other.
> I know there is GEOquery package, but I believe this is only for 
> retrieving data from GEO.

Henrik,

You are correct in assuming that GEOquery only retrieves data from GEO.  I have thought about trying to make some tools for submission, but I don't see an easy way to make these general.  In addition, much of the data that we store in Bioc data structures is already processed; GEO benefits from including as much raw data as possible and these data are not available in an expression data set.

In practice, we use a set of scripts (perl, in this case, but R would work just fine) to produce the SOFT format files from a set of "spreadsheets"
that describe the files, their subsets, etc.  The GEO website describes the formats necessary to produce--they are not that complicated.  For each project and array format, we modify things slightly, but the gist remains the same.  However, there are enough variations in file formats and experimental designs that producing a "fully automated" set of scripts for doing GEO submissions is quite challenging.

Sean