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

[ecsi at gmx.net]

Hi Sean,

> From what you have described so far, an ExpressionSet will suffice.  I 
> don't think there is a need for a MethyLumiSet since you describe 
> simply getting the normalized data from the GSE.

Well, I am still not really sure. Initially I wanted to download the raw 
data whereever available. Then we decided to use the soft files for all 
GEO series to make the task a bit easier, and because I was told that it 
should be okay to use already normalized data sets in case of 
methylation data. However, this is not really a Bioconductor question 
and maybe I should talk to my supervisor again about this ... it is the 
first time I work with methylation data ...

> I'd suggest going the route that Jim outlined using GSEMatrix files 
> and moving forward from there.

I tried this, but then some files get downloaded to another directory 
and not to the one I have got to use. All data have to be downloaded to 
a mapped network drive and must not be downloaded to C:/ (see my reply 
to Jims message).

> If you can fill in details of what downstream analysis you want to do 
> with the data, perhaps we can be more directive on that point.

Well, so far our general plan is to conduct region-based differential 
methylation analysis, but also to investigate for example differential 
methylation of enhancers with known long distance chromosomal 
interactions, the correlation/relationship to gene expression data and 
many other things. But I think it won't be a problem to later get the 
data from  Expressionsets and put it into MethyLumiSets or whatever 
necessary.

Best,
Simone