On Fri, Oct 8, 2010 at 6:47 PM, S T <elengss@gmail.com> wrote:

> Hello,
>
> I am an absolute beginner in using bioconductor. I would really appreciate
> some help if you have time. Thanks very much in advance.
>
> I have been trying to access a GSE file from GEO using GEOquery.
> I got the same error message as reported by David Martin on 8 June 2010.
>
> > gse <- getGEO(filename = system.file ("extdata/GSE20080_family.soft.gz",
> + package = "GEOquery"))
>
>
Hello.

You have the right function, but what you are doing above will try to load
data from a file on your computer.  Just do:

gse <- getGEO('GSE20080')

This will fetch the data from NCBI GEO.

Sean


> Error in read.table(con, sep = "\t", header =
> FALSE, nrows = nseries) :
>  invalid 'nlines' argument
> In addition: Warning messages:
> 1: In file(fname, "r") :
>  file("") only supports open = "w+" and open =
>
> "w+b": using the former
> 2: In file(con, "r") :
>  file("") only supports open = "w+" and open =
>
> "w+b": using the former
> 3: In file(fname, "r") :
>  file("") only supports open = "w+" and open =
>
> "w+b": using the former
> >
>
> I think the archived help file is here
> https://stat.ethz.ch/pipermail/bioconductor/2010-June/033876.html
> It mentions file location...
> Sorry, I'm not sure how to resolve this problem with file location...
> Do I need to download the file from GEO first?
>
> Sorry for being so ignorant.
> Thanks a lot.
>
> ENS
>
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