[BioC] GEOquery : 'cannot open URL'

[Sean Davis]

On Friday 29 September 2006 11:51, Chaitanya Acharya wrote:
> Glazko, Galina <Galina_Glazko at ...> writes:
> > Dear all,
> >
> > When I am trying to use GEOquery package, I get an error message:
> > > gse <- getGEO("GSE1132")
> >
> > trying URL
> > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE462_family.soft.gz
> > '
> >
> > Error in download.file(myurl, destfile, mode = mode) :
> >
> >         cannot open URL
> > 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE462_family.soft.gz
> > '
> >
> > May be I have to update the package or reinstall?
> >
> > Thank you!
> >
> > Galina
> >
> > 	[[alternative HTML version deleted]]
> >
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>
>
>
> Hi Galina,
> There is a way to ovecome this problem.
> Follow these steps:
>
> 1. Open GEOquery directory under "C:\Program
> Files\R\R-2.2.1\library\GEOquery" 2. Open R. You should notice 'GEOquery'
> file.
> 3. Open it is a text editor (Notepad, Wordpad etc). Scroll the file to
> line#309. 4. You are in getGEOfile function. You should notice blocks of
> code that give specific instructions depending on the file type. At ln 309,
> change the ftp URL to: gseurl <-
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/' 5. Save the
> file...and you should be set. It worked for me. If you have problems again,
> probably you might want to restart R.

Hi, Chaitanya.  

Note that simply updating GEOquery will fix this problem.

Sean