Hi Sean,

Thanks for your help and for your effort in developing this useful tool. I
have tried now and it works fine. I was able to create the exprSet object
(followed vignette) from GSE. There are few things that I didn't understand.
I would appreciate your help in this.

1. When I looked at VALUE, it is mentioned that 'Log Ratio (not used)'. What
does this mean? BTW, this 2 color cDNA data set.

2. Since, all the samples of from GPL2000, I tried to use getGEO("GPL2000")
to access gene information for this chip. But i don't know how to extract
this info from GPL. Could you please provide some  info on this issue.

Thanks again for your help.

Regards,
Sharon

On 4/18/06, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> 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@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
>
>
>

	[[alternative HTML version deleted]]

