On Tue, May 29, 2012 at 9:18 AM, Simone [guest] <guest@bioconductor.org>wrote:

>
> Hi!
>
> Currently I am trying to use the library "GEOquery" to retrieve meta
> information (phenodata information) and the data tables of GEO samples
> (from GEO series without GEO datasets).
>
> I already have got the data (.soft.gz files), so I tried it the following
> way for example:
>
> GSE19711 <- getGEO(filename=system.file("mypath/GSE19711_family.soft.gz",
> package="GEOquery"))
>
>
Hi, Simone.

The "system.file" part of your command above is not necessary (and is
probably the problem).  System.file is for locating files that came with a
specific software package.  So, you want something like:

GSE19711 <- getGEO('mypath/GSE19711_family.soft.gz')

Note that you will have to do a fair bit of work to get the data out of a
SOFT format file.  Instead, you should consider using a GSEMatrix file.
 Alternatively, download the raw data and use a platform-appropriate
package to read in and analyze the data.  Finally, note that you do not
need to download files separately.

You can use GEOquery to download and even make a repository of GEO files.

GSE19711 <- getGEO('GSE19711',destdir='mypath')

Executing the command above again will not download the file again.

Sean



> But I get the following error:
>
> 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 tried it on windows and linux and also with the newest version of R and
> GEOquery.
>
> On both machines there occurs the same error, also with other GEO
> accession numbers.
>
> What is going wrong and what can I do to get the information I need?
>
> When I use a path to my file which is not existing, I get the same error,
> but I am quite sure that I set the working directory and path to the GEO
> file correctly.
>
> Greets,
> Simone
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=German_Austria.1252  LC_CTYPE=German_Austria.1252
>  LC_MONETARY=German_Austria.1252
> [4] LC_NUMERIC=C                    LC_TIME=German_Austria.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.23.3     Biobase_2.16.0      BiocGenerics_0.2.0
>  BiocInstaller_1.4.4
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1
>
> > sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
>  LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.21.9 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1 tools_2.14.1 XML_3.9-4
>
> > traceback()
> 6: read.table(con, sep = "\t", header = FALSE, nrows = nseries)
> 5: withCallingHandlers(expr, warning = function(w)
> invokeRestart("muffleWarning"))
> 4: suppressWarnings(read.table(con, sep = "\t", header = FALSE,
>       nrows = nseries))
> 3: parseGSEMatrix(fname)
> 2: parseGEO(filename, GSElimits)
> 1: getGEO(filename =
> system.file("homo_sapiens/peripheral_whole_blood/GSE19711/GSE19711_family.soft.gz",
>       package = "GEOquery"))
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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