Hello, I am an absolute beginner in using bioconductor. I would really appreciate some help if you have time. Thanks very much in advance. I have been trying to access a GSE file from GEO using GEOquery. I got the same error message as reported by David Martin on 8 June 2010. > gse <- getGEO(filename = system.file ("extdata/GSE20080_family.soft.gz", + package = "GEOquery")) 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 > I think the archived help file is here https://stat.ethz.ch/pipermail/bioconductor/2010-June/033876.html It mentions file location... Sorry, I'm not sure how to resolve this problem with file location... Do I need to download the file from GEO first? Sorry for being so ignorant. Thanks a lot. ENS [[alternative HTML version deleted]]

On Fri, Oct 8, 2010 at 6:47 PM, S T <elengss@gmail.com> wrote: > Hello, > > I am an absolute beginner in using bioconductor. I would really appreciate > some help if you have time. Thanks very much in advance. > > I have been trying to access a GSE file from GEO using GEOquery. > I got the same error message as reported by David Martin on 8 June 2010. > > > gse <- getGEO(filename = system.file ("extdata/GSE20080_family.soft.gz", > + package = "GEOquery")) > > Hello. You have the right function, but what you are doing above will try to load data from a file on your computer. Just do: gse <- getGEO('GSE20080') This will fetch the data from NCBI GEO. Sean > 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 > > > > I think the archived help file is here > https://stat.ethz.ch/pipermail/bioconductor/2010-June/033876.html > It mentions file location... > Sorry, I'm not sure how to resolve this problem with file location... > Do I need to download the file from GEO first? > > Sorry for being so ignorant. > Thanks a lot. > > ENS > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Thank you so much! The GUI now reads File stored at: C:\DOCUME~1\AdminNUS\LOCALS~1\Temp\Rtmp4MN2u9/GPL8490.soft Warning message: closing unused connection 3 () > Will I be able to use the methylumi package to read and analyse this type of data? Sorry, I read through the methylumi pdf but could not really find out how to start using data downloaded from GEO. Sorry again for being stupid. Esther Ng On Sat, Oct 9, 2010 at 6:47 AM, S T <elengss@gmail.com> wrote: > Hello, > > I am an absolute beginner in using bioconductor. I would really appreciate > some help if you have time. Thanks very much in advance. > > I have been trying to access a GSE file from GEO using GEOquery. > I got the same error message as reported by David Martin on 8 June 2010. > > > gse <- getGEO(filename = system.file ("extdata/GSE20080_family.soft.gz", > + package = "GEOquery")) > > 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 > > > > I think the archived help file is here > https://stat.ethz.ch/pipermail/bioconductor/2010-June/033876.html > It mentions file location... > Sorry, I'm not sure how to resolve this problem with file location... > Do I need to download the file from GEO first? > > Sorry for being so ignorant. > Thanks a lot. > > ENS > > [[alternative HTML version deleted]]