[BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")

[ecsi at gmx.net]

Hi Jim,

> Why are you using system.file() in this context? 

Because there is an example in the GEOquery vignette ("2 Getting Started 
using GEOquery") which does it like this.

> Did you really download the soft file to your GEOquery library 
> directory? That seems odd to me.

I downloaded it to a local data repository in our network (it is 
obligatory to do it this way in this case).

Why does it seem odd to you? Because I downloaded the soft file? This 
was a recommendation of a colleague who works a lot with GEO, we thought 
the soft files would be the best option because they contain all the 
information available and furthermore they are available for all the GEO 
series I have analyze. As I already wrote in reply to the answer of 
Sean, if there is any better way to do it, I will be happy to hear about it!

Best,
Simone