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.UT F- 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 [[alternative HTML version deleted]]

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;L C_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