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

[Sean Davis]

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