[BioC] getGEO

[Sean Davis]

On Friday 03 November 2006 13:17, Weiwei Shi wrote:
> hi,
>
> I am a newbie using this GEOquery package and have a couple of issues
> when I used it:
> 2. When I used
> getGEO("GSE3210")
> then there is a kind of connection problem. I am wondering how to correct
> this?

You will need to use the version from 1.9 or 2.0 (devel) of Bioconductor.  The 
URL for GEO changes relatively regularly, which is what causes this problem.

> 3. When I download the gz file and run it locally,
> it seems working but ends with a couple of warnings (shown below). Is it
> ok?

This has to do with the encoding in the file being incorrect.  This isn't 
SUPPOSED to happen, but I have seen this also.  You may have to do some 
simple checks to make sure that you have all the samples represented, etc.

> 4. BTW, it is really slow, even running from local. Should gunzipping
> at first help?

I'm not sure what you mean by slow, but it is parsing a 4.7 million line file, 
so that may take a while.  Gunzipping will not help significantly--sorry.

Sean