Dear sir or madam, I am trying to import gene expression data(GDS or GSM) with getGEO function in R with the following command: gds <- getGEO(filename=system.file("extdata/GDS4457.soft.gz",package="GEOquer y")) Unfortunately I get the 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 Would you please advise me what to do? Regards Nazanin Hosseinkhan [[alternative HTML version deleted]]

Dear Nazanin, I would try: gds <-getGEO("GDS4457") Best, Simona On Sun, Dec 1, 2013 at 8:38 AM, Nazanin Hosseinkhan < Hosseinkhan@ibb.ut.ac.ir> wrote: > > Dear sir or madam, > I am trying to import gene expression data(GDS or GSM) with getGEO function > in R with the following command: > gds <- > getGEO(filename=system.file("extdata/GDS4457.soft.gz",package="GEOqu ery")) > Unfortunately I get the 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 > > Would you please advise me what to do? > Regards > Nazanin Hosseinkhan > > > > > [[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 > -- -- Dr. Simona Rossi Bioinformatician SIB | Swiss Institute of Bioinformatics [[alternative HTML version deleted]]