[BioC] Arguments to getGEO?

[Sean Davis]

On Tue, Sep 9, 2008 at 2:14 PM, Thomas Hampton
<Thomas.H.Hampton at dartmouth.edu> wrote:
> The pdf documentation that comes with GEOquery suggests that
> getGEO can take GSEMatrix as an argument, while getGEO itself does not.
>
>
> Here is what the pdf says:
>
> 4.1 Getting GSE Series Matrix files as an ExpressionSet
> GEO Series are collections of related experiments. In addition to
> being available as SOFT
> format files, which are quite large, NCBI GEO has prepared a simpler
> format file based on
> tab-delimited text. The getGEO function can handle this format and
> will parse very large
> GSEs quite quickly. The data structure returned from this parsing is
> a list of ExpressionSets.
> As an example, we download and parse GSE2553.
>  > gse2553 <- getGEO("GSE2553", GSEMatrix = TRUE)
> Found 1 file(s)
> GSE2553_series_matrix.txt.gz
> File stored at:
> /tmp/Rtmpebe3Oh/GPL1977.soft
>  > show(gse2553)
> ...
>
> But getGEO does not actually list "GSEMatrix" as an argument:
>
> getGEO               package:GEOquery               R Documentation
>
> Get a GEO object from NCBI or file
>
> Description:
>
>      This function is the main user-level function in the GEOquery
>      package.  It directs the download (if no filename is specified)
>      and parsing of a GEO SOFT format file into an R data structure
>      specifically designed to make access to each of the important
>      parts of the GEO SOFT format easily accessible.
>
> Usage:
>
>      getGEO(GEO = NULL, filename = NULL, destdir = tempdir(),
> GSElimits=NULL)
>
>
> As a result, I get this error:
>
>  > gse <- getGEO("GSE462", GSEMatrix = FALSE)
> Error in getGEO("GSE462", GSEMatrix = FALSE) :
>         unused argument(s) (GSEMatrix = FALSE)
>
>
>
>  > sessionInfo()
> R version 2.5.0 (2007-04-23)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
> TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
> 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID
> ENTIFICATION=C
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"
> "methods"
> [7] "base"
>
> other attached packages:
> GEOquery
>  "2.0.6"

Hi, Tom.  Simple answer--upgrade R and GEOquery.  You need to be using
GEOquery 2.4.5 or later, available for R 2.7.x and bioconductor 2.2
release.

Sean