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"


Any ideas, Sean?

Thanks,

Tom


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