[BioC] GEOquery : 'cannot open URL'

[Chaitanya Acharya]

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. 

But I must tell you that it takes a long time to load the GSE dataset...have
patience.

Thanks,
Chaitanya