[BioC] Error with GEOquery

[Sean Davis]

Hi, Sharon.

It turns out that you found a bug in the way that GEO was preparing their
GSE files.  GSE2718 is fixed now and you should be able to use GEOquery
again.  If others see the same error, GEO passed along that the other GSE
files should be fixed within a few days.

As for using an already-downloaded file, see the "filename" argument in the
getGEO() help.  This will allow you to specify a filename of a previously
downloaded file.

Sean


On 4/11/06 4:54 AM, "Sharon" <sharonanandhi at gmail.com> wrote:

> Hi Sean,

I am trying to use GEOquery to download GSE data files from GEO.
> When
I tried, I am getting the following error:

gse <-
> getGEO("GSE2718")

trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2718/GSE2718_family.soft
> .gz'
ftp data connection made, file length 23892634 bytes
opened
> URL
downloaded 23332Kb

File stored
> at:
C:\DOCUME~1\Anbarasu\LOCALS~1\Temp\Rtmp8707/GSE2718.soft.gz
Parsing....
^P
> LATFORM = GPL2000
^SAMPLE = GSM49820
^SAMPLE = GSM65592
Error in
> regexpr(pattern, text, extended, fixed, useBytes) :
        invalid
> argument

my sessionInfo:

R version 2.2.0, 2005-10-06,
> i386-pc-mingw32

attached base packages:
[1] "methods"   "stats"
> "graphics"  "grDevices" "utils"    
"datasets"  "base"

other attached
> packages:
GEOquery
 "1.5.6"

Is it due to my R 2.2.0? I am using GEOquery on
> Windows XP with 1GB RAM.

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

Thanks in advance.

Regards,
Sharon