[BioC] GEOquery

Sean Davis sdavis2 at mail.nih.gov
Thu Jul 20 20:45:11 CEST 2006

On 7/19/06 10:44, "LUIS F MENEZES" <lmenezes at jhmi.edu> wrote:

> Hi, 
> I am using version 1.6.0 of GEOquery but GDS2eSet function seems not to be
> working properly. It tries to use "Table", which does not exist. I replaced it
> for "table", but it still does not work. I am also not sure if getGEO is
> retrieving the information in a correct format, because I cannot access the
> different GSMs of the downloaded GSE file (GSE3219), even though they are
> present.


The function GDS2eSet works on a GDS object, not a GSE object.  For GSE3219,
there is no GDS, so you GDS2eSet cannot be used to make the eSet.  There is
an example in the vignette for GEOquery that shows some code for making an
eSet from a GSE object.

Hope that clarifies things a bit.


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