[BioC] Error with GEOquery

[Peter (BioC)]

Sharon wrote:
> And, another related question is: How can I use *getGEO() * with the
> already downloaded GSE2718.soft.gz  file (to avoid subsequent
> downlaoding).

Use the filename argument to getGEO to parse and existing file, rather 
than downloading it again.  For example:

library(Biobase)
library(GEOquery)

#Download GEO file, put it in the current directory, and load it:
gse <- getGEO('GSE2718', destdir=".")

#Or, open an existing GEO file (even if its compressed):
gse <- getGEO(filename='GSE2718.soft.gz')

Peter