[BioC] GEOquery: getGEO() doesn\'t work (error \"invalid \'nlines\' argument\")
ecsi at gmx.net
ecsi at gmx.net
Wed May 30 11:38:10 CEST 2012
> 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
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