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

ecsi at gmx.net ecsi at gmx.net
Wed May 30 11:49:09 CEST 2012

> 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 ...

Okay, we've talked it over again and things changed. I need the raw 
data. So maybe the best way would be to create ExpressionSets with 
getGEO() to have all the sample meta information, manipulate the 
phenodata of the ExpressionSets the way I need them, download the RAW 
data with getGEOSuppFiles(), normalize it the way we want to do it and 
then put these data into the ExpressionSets I have got.

Still, I have the problem that not all files get downloaded to the 
directory I set for destdir. The series_matrix files are downloaded to 
the correct directory, but some other files always land on the Temp 
directory in C:/

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