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Question: Arguments to getGEO?
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gravatar for Thomas Hampton
10.1 years ago by
Thomas Hampton740 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.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]]
ADD COMMENTlink modified 10.1 years ago by Sean Davis21k • written 10.1 years ago by Thomas Hampton740
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gravatar for Sean Davis
10.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 10.1 years ago by Sean Davis21k
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