Hi everyone, I would like to get a data (e.g. "GSE20986") from GEO using getGEO. And then start analyzing the the data by different packages/functions in the "biocuonductor" to get the differentially expressed genes. For the first step, I used this (http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery/ inst/doc/GEOquery.R)<http: www.bioconductor.org="" packages="" release="" bioc="" vignettes="" geoquery="" inst="" doc="" geoquery.r=""> . When I ran following line: gse <- getGEO(filename=system.file("extdata/GSE8500_family.soft.gz",package=" GEOquery")) I got this 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 ---------------------------------------------------------------------- ------------------------------------------------------------- May someone send me a script that I could do all these steps to get the differentially expressed genes? Thanks, Jerry [[alternative HTML version deleted]]

if(!require('GEOquery')) biocLite('GEOquery') library(GEOquery) foo <- getGEO('GSE20986')[[1]] ## since there's only one dataset show(foo) ## ExpressionSet (storageMode: lockedEnvironment) ## assayData: 54675 features, 12 samples ## ... Statistics is the grammar of science. Karl Pearson <http: en.wikipedia.org="" wiki="" the_grammar_of_science=""> On Thu, Feb 13, 2014 at 10:50 AM, Jerry Cholo <jerrycholo@gmail.com> wrote: > Hi everyone, > > I would like to get a data (e.g. "GSE20986") from GEO using getGEO. And > then start analyzing the the data by different packages/functions in the > "biocuonductor" to get the differentially expressed genes. For the first > step, I used this > ( > http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery /inst/doc/GEOquery.R > )< > http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery /inst/doc/GEOquery.R > > > . > > When I ran following line: > > gse <- > > getGEO(filename=system.file("extdata/GSE8500_family.soft.gz",package ="GEOquery")) > > I got this 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 > > > -------------------------------------------------------------------- --------------------------------------------------------------- > > May someone send me a script that I could do all these steps to get the > differentially expressed genes? > > Thanks, > > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

On Thu, Feb 13, 2014 at 1:50 PM, Jerry Cholo <jerrycholo@gmail.com> wrote: > Hi everyone, > > I would like to get a data (e.g. "GSE20986") from GEO using getGEO. And > then start analyzing the the data by different packages/functions in the > "biocuonductor" to get the differentially expressed genes. For the first > step, I used this > ( > http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery /inst/doc/GEOquery.R > )< > http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery /inst/doc/GEOquery.R > > > . > > When I ran following line: > > gse <- > > getGEO(filename=system.file("extdata/GSE8500_family.soft.gz",package ="GEOquery")) > > There is no need for the system.file() stuff. That is simply used to build the documentation. I should clean that up in the vignette. In any case, here is what you want: eset = getGEO('8500')[[1]] > I got this 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 > > > -------------------------------------------------------------------- --------------------------------------------------------------- > > May someone send me a script that I could do all these steps to get the > differentially expressed genes? > > Thanks, > > Jerry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]